Windows 7 administrator: can't restart, shutdown, execute anything

Hi all,
I have Windows Seven Ultimate running on a machine just fine for about half a year. After installing some piece of software related to android rooting, I found myself unable to do anything on the computer, as launch windows explorer, restart shutdown, start any other program, as this error appears:
Windows cannot access the specified device, path, or file. You may not have the appropriate permissions to access the item.
Watch this: Windows 7 error: you may not have the appropriate permissions to access the item - YouTube

I rebooted by power cycle into Safe mode. There I didn't encountered any problems, I was able to start programs, I uninstalled the latest software I installed before this problem, but this didn't solved the problem.
Also, while in Safe Mode, I created another admin user but is behaves the same way as the original user I have on this machine.

Anyone saw this before?

Have you tried a system restore to a point before you installed this software?

A full anti-virus scan in Safe Mode won't do any harm, for which Malwarebytes is very good at.

Malwarebytes : Free anti-malware, anti-virus and spyware removal download

If you can't run Malwarebytes in Safe Mode, then download and burn to CD or flash stick, boot and scan with Microsoft Standalone System Sweeper

Once it's clean boot the DVD Repair console or Repair CD to run Startup Repair repeatedly, which should automate System Restore and SFC. But if not run SysRestore from |Recovery Tools list, and SFC from Command Line in tools list: SFC -SCANNOW Run in Command Prompt at Boot

If you can get into Win7 and regain some functionality but not all, then run a Repair Install

If all fails, copy out your data - if necessary using Paragon Rescue CD - then run full Factory Recovery from boot or using Disks which came with computer, you made or order from manufacturer. Or find a Win7 installer for your version to clean reinstall using tips to get a perfect reinstall in my signature box below:

Thanks seavixen32, but since I got this issue already last week and spent some time troubleshooting it, I forgot to mention:
In safe mode I succeeded in running a full system check with Avira Antivirus and with Malwarebytes and no threats were found.
As didn't enabled system restore before, I cannot use it for restore points.

gregrocker, I don't know if Startup Repair will do any good because this Windows OS is starting properly.
Does SFC comes from system file check? If so, I will give it a try with the guide you pointed above.
Running Repair Install seems like a good approach only if I could launch applications, as you already noted.

A perfect reinstall is my last option.

I am interested in finding the cause of my problem so I won't run into it again.

Right click on the drive that you have w7 installed-properties-security

Are you the only user on this PC ?....Do you have parental controls activated?
start-type: lusrmgr.msc

Also try removing your user account password.

Hello,

I have 2 approaches for you. Try them one by one.

1) Your use profile may be corrupted, so try enabling the builtin admin from the install dvd or repair disk and then create a new user profile.

Windows 7 Administrator logon failed. "User Profile Service - Microsoft Answers

2) Boot from the install dvd or startup disk and restore a pristine copy of the registry from the Regback folder. See the later steps ( step 10 onwards) in this tut (dont get confused by the tut title).

Startup Repair Infinite Loop Recovery

As you said you couldn't run any programs, I suggested you run System File CHecker from the DVD/Repair CD Command Line so it doesn't rely on possibly-corrupt onboard system files.

Startup Repair automates SFC, System REstore and a dozen other tests and fixes which make it worth running as well if you have limited or no OS functionality.

A Repair Install is still worth trying since it is much more than runnning a Program.

Be sure to try the other approaches given as they all have merit.

As you want to find the cause before reinstalling, look for repeat errors in the logs and use the System Resources which might be available all presented in the Troubleshooting link in my signature box below: