Windows will not load/Startup repair cannot fix

I have a Sony Viao with Win 7 Home Premium and I just deleted some form of Trojan with MS Security Essentials and then I ran windows updates before I restarted the machine. Windows update installed some security updates along with Service pack 1 and IE9. Now the computer will not load Windows. It goes straight to the startup repair but cannot fix the problem. There is not restore points other that when SP1 was installed and I gives an error every time I try to restore it. I can get to a command prompt and I have tried to run sfc /scannow but it tells me there is a system repair pending which requires a reboot and then does nothing. I also tried check disk(just as a last chance) but that didn't do anything. Is there any other way that I can repair windows without re-installing windows?

I got a system restore error code of (0x8000ffff).

A few things to try:

• You can get into the Recovery Environment (RE) so all hope is not lost. In the RE, open the command prompt.
  1. Type
     diskpart
     and let Diskpart load.
  2. Type
     list disk
     and find the disk number corresponding the disk that your Windows system is on. It should be the only disk with a size attributed to it in a laptop.
  3. Then type
     select disk 0
     assuming your disk number is 0 (mine is).
  4. Now type
     list partition
     and make a note of which partition contains the operating system files (if you know what size your Windows partition is). Also make a note of whether there is a system reserved partition, usually with 100 or 200 MB in size. This is very important to get correct, so if you are not sure, ask us.
  5. If you have a system reserved partition with a size in the 100-200 MB range, choose that partition. Otherwise, choose the partition containing the Windows files.
  6. Type
     select partition 1
     assuming the partition containing the appropriate files is partition 1.
  7. Type
     active
     to mark that partition as active. This signifies that this partition which contains the boot/operating system files is now active.
  
  
  Now try running startup repair three times with a reboot between each. Startup Repair - Run 3 Separate Times
• How to use the Bootrec.exe tool in the Windows Recovery Environment to troubleshoot and repair startup issues in Windows
• Startup Repair Infinite Loop Recovery