Group Client Policy / Admin issues / links not working / files missing

Hi
2008 Dell Precision T7400 with Base Dual Intel Xeon E5420 (2.50GHz,1333FSB,2x6MB,Quad Core)
Memory 8GB, 667MHz, ECC Memory (8x1GB)
Video Card 512MB PCIe x16 nVidia Quadro FX 1700 (MRGA14L), Dual Monitor DVI or VGA Graphics Card
Hard Drive 320GB (7,200 rpm) SATA 3.0Gb/s Hard Drive with NCQ and 16MB DataBurst Cache™.
Windows 7 x64 Ultimate upgraded from XP Professional x64 Edition SP2 (NTFS) about a year or so ago.
Thursday I did a defrag and have no system restore point. The same night I updated Boinc BOINC and Oracle Virtualbox was also installed with it. The problems started after when I went to log in the next day.

First sign of a problem was getting a message windows could not connect to the Group Policy Client service. This problem prevents standard users from logging on to the system. As an administrative user, you can review the systems event log for details about why the service didn't respond. I am the admin but it won't let me view event logs, when I go to event viewer the icon is blank like the link is missing and it won't open. It is in the system32 folder though when I look for it but it won't open from there either. I can view it in safe mode but I have to open it by going to the Windows\system32 folder. Sorry forgot to take a note of what it says I'm running a full virus scan at the moment. I did find that topic about restoring/fixing group policy in Regedit but it was fine and I didn't have to fix it.

Malwarebytes found some malware in the Registry and they've been removed.
I tried to uninstall Oracle Virtualbox but it says I don't have permission to do that and in safe mode it cannot find the uninstaller even though it is there in the folder and I've checked its Registry and it is fine.
I have ran scf /scannow a few times, everythings fine.
Also have tried repair and few times.
Have ran chkdsk
In safe mode if I click on a link/shortcut for files it states for example %win%\xyz not found instead of c:\windows\xyz. In normal mode it lists the file c:\windows\xyz but states that 'system could not find the environment option that was entered'

I'm still googling for solutions but any assistance would be great.

Below is hijackit result. It did say it was denied write access to hosts files, if that info is of any use.
Even though it says below for example lsass.exe (file missing) if I go to c:\windows\system32 it is there.

Code:

 
Logfile of Trend Micro HijackThis v2.0.5
Scan saved at 19:16:02, on 08/03/2014
Platform: Windows 7 SP1 (WinNT 6.00.3505)
MSIE: Internet Explorer v11.0 (11.00.9600.16518)
CHROME: 33.0.1750.146
FIREFOX: 14.0.1 (en-GB)
Boot mode: Normal
 
Running processes:
C:\Program Files (x86)\Malwarebytes' Anti-Malware\mbamgui.exe
C:\Users\Colette\AppData\Local\Akamai\netsession_win.exe
C:\Users\Colette\AppData\Local\Akamai\netsession_win.exe
C:\Program Files (x86)\Adobe\Adobe Creative Cloud\ACC\Creative Cloud.exe
C:\Program Files (x86)\Common Files\Adobe\OOBE\PDApp\IPC\AdobeIPCBroker.exe
C:\Program Files (x86)\Adobe\Adobe Creative Cloud\CoreSyncV1\CoreSync.exe
C:\Program Files (x86)\Adobe\Adobe Creative Cloud\HEX\Adobe CEF Helper.exe
C:\Program Files (x86)\Adobe\Adobe Creative Cloud\HEX\Adobe CEF Helper.exe
C:\Program Files (x86)\Adobe\Adobe Creative Cloud\HEX\Adobe CEF Helper.exe
C:\Users\Colette\AppData\Local\Google\Chrome\Application\chrome.exe
C:\Users\Colette\AppData\Local\Google\Chrome\Application\chrome.exe
C:\Users\Colette\AppData\Local\Google\Chrome\Application\chrome.exe
C:\Users\Colette\AppData\Local\Google\Chrome\Application\chrome.exe
C:\Users\Colette\AppData\Local\Google\Chrome\Application\chrome.exe
C:\Users\Colette\AppData\Local\Google\Chrome\Application\chrome.exe
C:\Users\Colette\AppData\Local\Google\Chrome\Application\chrome.exe
C:\Users\Colette\AppData\Local\Google\Chrome\Application\chrome.exe
C:\Users\Colette\Documents\New folder\HijackThis.exe
 
R1 - HKCU\Software\Microsoft\Internet Explorer\Main,Default_Page_URL = MSN IE: Hotmail, Outlook, Skype, Entertainment, Sport & News
R1 - HKCU\Software\Microsoft\Internet Explorer\Main,Search Page = Bing
R0 - HKCU\Software\Microsoft\Internet Explorer\Main,Start Page = https://www.google.ie/
R1 - HKLM\Software\Microsoft\Internet Explorer\Main,Default_Page_URL = MSN.com
R1 - HKLM\Software\Microsoft\Internet Explorer\Main,Default_Search_URL = Bing
R1 - HKLM\Software\Microsoft\Internet Explorer\Main,Search Page = Bing
R0 - HKLM\Software\Microsoft\Internet Explorer\Main,Start Page = MSN.com
R0 - HKLM\Software\Microsoft\Internet Explorer\Search,SearchAssistant = 
R0 - HKLM\Software\Microsoft\Internet Explorer\Search,CustomizeSearch = 
R0 - HKLM\Software\Microsoft\Internet Explorer\Main,Local Page = C:\Windows\SysWOW64\blank.htm
R1 - HKCU\Software\Microsoft\Internet Explorer\Main,Window Title = Windows Internet Explorer provided by MSN and Bing
R1 - HKCU\Software\Microsoft\Windows\CurrentVersion\Internet Settings,ProxyOverride = *.local;<local>
R0 - HKCU\Software\Microsoft\Internet Explorer\Toolbar,LinksFolderName = 
R3 - URLSearchHook: Ashampoo US Toolbar - {124d001a-bdcb-472f-aa59-bbe7e4bc3204} - C:\Program Files (x86)\Ashampoo_US\prxtbAsha.dll
R3 - URLSearchHook: Yahoo! Toolbar - {EF99BD32-C1FB-11D2-892F-0090271D4F88} - C:\Program Files (x86)\Yahoo!\Companion\Installs\cpn\yt.dll
F2 - REG:system.ini: UserInit=userinit.exe,
O2 - BHO: &Yahoo! Toolbar Helper - {02478D38-C3F9-4efb-9B51-7695ECA05670} - C:\Program Files (x86)\Yahoo!\Companion\Installs\cpn\yt.dll
O2 - BHO: HP Print Enhancer - {0347C33E-8762-4905-BF09-768834316C61} - C:\Program Files (x86)\HP\Digital Imaging\Smart Web Printing\hpswp_printenhancer.dll
O2 - BHO: Ashampoo US - {124d001a-bdcb-472f-aa59-bbe7e4bc3204} - C:\Program Files (x86)\Ashampoo_US\prxtbAsha.dll
O2 - BHO: Groove GFS Browser Helper - {72853161-30C5-4D22-B7F9-0BBC1D38A37E} - C:\PROGRA~2\MICROS~2\Office14\GROOVEEX.DLL
O2 - BHO: Java(tm) Plug-In SSV Helper - {761497BB-D6F0-462C-B6EB-D4DAF1D92D43} - C:\Program Files (x86)\Java\jre7\bin\ssv.dll
O2 - BHO: Adobe Acrobat Create PDF Helper - {AE7CD045-E861-484f-8273-0445EE161910} - C:\Program Files (x86)\Common Files\Adobe\Acrobat\WCIEActiveX\AcroIEFavClient.dll
O2 - BHO: URLRedirectionBHO - {B4F3A835-0E21-4959-BA22-42B3008E02FF} - C:\PROGRA~2\MICROS~2\Office14\URLREDIR.DLL
O2 - BHO: Java(tm) Plug-In 2 SSV Helper - {DBC80044-A445-435b-BC74-9C25C1C588A9} - C:\Program Files (x86)\Java\jre7\bin\jp2ssv.dll
O2 - BHO: SmartSelect - {F4971EE7-DAA0-4053-9964-665D8EE6A077} - C:\Program Files (x86)\Common Files\Adobe\Acrobat\WCIEActiveX\AcroIEFavClient.dll
O2 - BHO: SingleInstance Class - {FDAD4DA1-61A2-4FD8-9C17-86F7AC245081} - C:\Program Files (x86)\Yahoo!\Companion\Installs\cpn\YTSingleInstance.dll
O2 - BHO: HP Smart BHO Class - {FFFFFFFF-CF4E-4F2B-BDC2-0E72E116A856} - C:\Program Files (x86)\HP\Digital Imaging\Smart Web Printing\hpswp_BHO.dll
O3 - Toolbar: Ashampoo US Toolbar - {124d001a-bdcb-472f-aa59-bbe7e4bc3204} - C:\Program Files (x86)\Ashampoo_US\prxtbAsha.dll
O3 - Toolbar: Yahoo! Toolbar - {EF99BD32-C1FB-11D2-892F-0090271D4F88} - C:\Program Files (x86)\Yahoo!\Companion\Installs\cpn\yt.dll
O3 - Toolbar: Adobe Acrobat Create PDF Toolbar - {47833539-D0C5-4125-9FA8-0819E2EAAC93} - C:\Program Files (x86)\Common Files\Adobe\Acrobat\WCIEActiveX\AcroIEFavClient.dll
O4 - HKLM\..\Run: [SwitchBoard] C:\Program Files (x86)\Common Files\Adobe\SwitchBoard\SwitchBoard.exe
O4 - HKLM\..\Run: [AdobeCS6ServiceManager] "C:\Program Files (x86)\Common Files\Adobe\CS6ServiceManager\CS6ServiceManager.exe" -launchedbylogin
O4 - HKLM\..\Run: [AdobeCS4ServiceManager] "C:\Program Files (x86)\Common Files\Adobe\CS4ServiceManager\CS4ServiceManager.exe" -launchedbylogin
O4 - HKLM\..\Run: [Adobe Creative Cloud] "C:\Program Files (x86)\Adobe\Adobe Creative Cloud\ACC\Creative Cloud.exe" --showwindow=false --onOSstartup=true
O4 - HKLM\..\Run: [Adobe ARM] "C:\Program Files (x86)\Common Files\Adobe\ARM\1.0\AdobeARM.exe"
O4 - HKLM\..\RunOnce: [Malwarebytes Anti-Malware] C:\Program Files (x86)\Malwarebytes' Anti-Malware\mbamgui.exe /install /silent
O4 - HKLM\..\RunOnce: [Malwarebytes Anti-Malware (cleanup)] rundll32.exe "C:\ProgramData\Malwarebytes\Malwarebytes' Anti-Malware\cleanup.dll",ProcessCleanupScript
O4 - HKCU\..\Run: [Prime95] C:\Users\Colette\Downloads\p95v279.win64\prime95.exe
O4 - HKCU\..\Run: [Akamai NetSession Interface] "C:\Users\Colette\AppData\Local\Akamai\netsession_win.exe"
O8 - Extra context menu item: Add to Google Photos Screensa&ver - res://C:\Windows\system32\GPhotos.scr/200
O8 - Extra context menu item: E&xport to Microsoft Excel - res://C:\PROGRA~2\MICROS~2\Office14\EXCEL.EXE/3000
O8 - Extra context menu item: Se&nd to OneNote - res://C:\PROGRA~2\MICROS~2\Office14\ONBttnIE.dll/105
O9 - Extra button: Send to OneNote - {2670000A-7350-4f3c-8081-5663EE0C6C49} - C:\Program Files (x86)\Microsoft Office\Office14\ONBttnIE.dll
O9 - Extra 'Tools' menuitem: Se&nd to OneNote - {2670000A-7350-4f3c-8081-5663EE0C6C49} - C:\Program Files (x86)\Microsoft Office\Office14\ONBttnIE.dll
O9 - Extra button: OneNote Lin&ked Notes - {789FE86F-6FC4-46A1-9849-EDE0DB0C95CA} - C:\Program Files (x86)\Microsoft Office\Office14\ONBttnIELinkedNotes.dll
O9 - Extra 'Tools' menuitem: OneNote Lin&ked Notes - {789FE86F-6FC4-46A1-9849-EDE0DB0C95CA} - C:\Program Files (x86)\Microsoft Office\Office14\ONBttnIELinkedNotes.dll
O9 - Extra button: Show or hide HP Smart Web Printing - {DDE87865-83C5-48c4-8357-2F5B1AA84522} - C:\Program Files (x86)\HP\Digital Imaging\Smart Web Printing\hpswp_BHO.dll
O11 - Options group: [ACCELERATED_GRAPHICS] Accelerated graphics
O15 - Trusted Zone: *.dell.com
O16 - DPF: {D27CDB6E-AE6D-11CF-96B8-444553540000} (Shockwave Flash Object) - http://fpdownload2.macromedia.com/ge...sh/swflash.cab
O18 - Filter hijack: text/xml - {807573E5-5146-11D5-A672-00B0D022E945} - C:\Program Files (x86)\Common Files\Microsoft Shared\OFFICE14\MSOXMLMF.DLL
O23 - Service: Adobe Acrobat Update Service (AdobeARMservice) - Adobe Systems Incorporated - C:\Program Files (x86)\Common Files\Adobe\ARM\1.0\armsvc.exe
O23 - Service: @%SystemRoot%\system32\Alg.exe,-112 (ALG) - Unknown owner - C:\Windows\System32\alg.exe (file missing)
O23 - Service: @%SystemRoot%\system32\efssvc.dll,-100 (EFS) - Unknown owner - C:\Windows\System32\lsass.exe (file missing)
O23 - Service: @gpapi.dll,-112 (gpsvc) - Unknown owner - C:\Windows\
O23 - Service: HQueueClient - Unknown owner - C:\HQueueClient\hqclientservice.exe
O23 - Service: HQueueServer - Unknown owner - C:\HQueueServer\hqserverservice.exe
O23 - Service: @%SystemRoot%\system32\ieetwcollectorres.dll,-1000 (IEEtwCollectorService) - Unknown owner - C:\Windows\system32\IEEtwCollector.exe (file missing)
O23 - Service: @keyiso.dll,-100 (KeyIso) - Unknown owner - C:\Windows\system32\lsass.exe (file missing)
O23 - Service: MBAMScheduler - Malwarebytes Corporation - C:\Program Files (x86)\Malwarebytes' Anti-Malware\mbamscheduler.exe
O23 - Service: MBAMService - Malwarebytes Corporation - C:\Program Files (x86)\Malwarebytes' Anti-Malware\mbamservice.exe
O23 - Service: @comres.dll,-2797 (MSDTC) - Unknown owner - C:\Windows\System32\msdtc.exe (file missing)
O23 - Service: @%SystemRoot%\System32\netlogon.dll,-102 (Netlogon) - Unknown owner - C:\Windows\system32\lsass.exe (file missing)
O23 - Service: NVIDIA Display Driver Service (nvsvc) - Unknown owner - C:\Windows\system32\nvvsvc.exe (file missing)
O23 - Service: NVIDIA WMI Provider (NVWMI) - Unknown owner - C:\Windows\system32\nvwmi64.exe (file missing)
O23 - Service: @%systemroot%\system32\psbase.dll,-300 (ProtectedStorage) - Unknown owner - C:\Windows\system32\lsass.exe (file missing)
O23 - Service: @%SystemRoot%\system32\qwave.dll,-1 (QWAVE) - Unknown owner - C:\Windows\
O23 - Service: @%systemroot%\system32\Locator.exe,-2 (RpcLocator) - Unknown owner - C:\Windows\system32\locator.exe (file missing)
O23 - Service: @%SystemRoot%\system32\samsrv.dll,-1 (SamSs) - Unknown owner - C:\Windows\system32\lsass.exe (file missing)
O23 - Service: @%SystemRoot%\system32\seclogon.dll,-7001 (seclogon) - Unknown owner - C:\Windows\
O23 - Service: @%SystemRoot%\system32\snmptrap.exe,-3 (SNMPTRAP) - Unknown owner - C:\Windows\System32\snmptrap.exe (file missing)
O23 - Service: @%systemroot%\system32\spoolsv.exe,-1 (Spooler) - Unknown owner - C:\Windows\System32\spoolsv.exe (file missing)
O23 - Service: @%SystemRoot%\system32\sppsvc.exe,-101 (sppsvc) - Unknown owner - C:\Windows\system32\sppsvc.exe (file missing)
O23 - Service: Adobe SwitchBoard (SwitchBoard) - Adobe Systems Incorporated - C:\Program Files (x86)\Common Files\Adobe\SwitchBoard\SwitchBoard.exe
O23 - Service: @%SystemRoot%\system32\ui0detect.exe,-101 (UI0Detect) - Unknown owner - C:\Windows\system32\UI0Detect.exe (file missing)
O23 - Service: @%SystemRoot%\system32\vaultsvc.dll,-1003 (VaultSvc) - Unknown owner - C:\Windows\system32\lsass.exe (file missing)
O23 - Service: @%SystemRoot%\system32\vds.exe,-100 (vds) - Unknown owner - C:\Windows\System32\vds.exe (file missing)
O23 - Service: @%systemroot%\system32\vssvc.exe,-102 (VSS) - Unknown owner - C:\Windows\system32\vssvc.exe (file missing)
O23 - Service: @%SystemRoot%\system32\Wat\WatUX.exe,-601 (WatAdminSvc) - Unknown owner - C:\Windows\system32\Wat\WatAdminSvc.exe (file missing)
O23 - Service: @%systemroot%\system32\wbengine.exe,-104 (wbengine) - Unknown owner - C:\Windows\system32\wbengine.exe (file missing)
O23 - Service: @%Systemroot%\system32\wbem\wmiapsrv.exe,-110 (wmiApSrv) - Unknown owner - C:\Windows\system32\wbem\WmiApSrv.exe (file missing)
O23 - Service: @%PROGRAMFILES%\Windows Media Player\wmpnetwk.exe,-101 (WMPNetworkSvc) - Unknown owner - C:\Program Files (x86)\Windows Media Player\wmpnetwk.exe (file missing)
 
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