I am running Windows 7 Ultimate 64 bit with Bitdefender 2010 Antivirus. Was affected by the trojan.fakealert.5 issue.
Steps which I took to fix the issue:
1) Stop Bitdefender (BD) Realtime Protection immediately
2) Update BD with Engine 7.30848 and Virus Signatures 5474032
3) Went into DB Antivirus tab -> Quarantine and restored whatever trojan.fakealert.5 files were there
4) For files which cannot be restored as a message saying the file is already there or the path not found here is a possible fix
5) Restore the files to a different directory using the "Browse" button. Make sure take note the original directory before restoring it to a different directory. In my case, for all c:\windows\system32 files I copied them to c:\system32 and for c:\windows\syswow64 files I copied them to c:\syswow64. The quarantined files should not be on your list any more after restoring. The objective here is to copy them back to their original folders as many of the files are shown as empty shells (they have 0KB) so you need to copy the normal ones back to the system folders.
6) Next, I restarted Windows using my Windows 7 DVD and click Repair and click Command Prompt. The reason why you need to use a DVD is because many of the restored system files are in use by Windows and it will not allow you to copy over them. Using command prompt I copied the files back to the original folders and then restarted Windows.
My Windows 7 is working more normal now. I didn't realise that after the system files were quarantined, Windows or BD placed empty shells of files with the same name in the system directories. It caused problems with a few of my programs.
Enjoy.