As reported in a monstrous 63 page topic created yesterday at the BitDefender forums, users of 64-bit Windows stated that BitDefender was suddenly flagging their clean and required Windows system files as the Trojan.FakeAlert.5 infection. If a user had their scan settings to automatically quarantine infected files, these files would then be automatically moved to BitDefender's quarantine. As many of these files are Windows system files that are required for Windows to operate correctly, Windows would no longer function or became unbootable.
BitDefender has issued a press release describing what happened and information about a patch that can be downloaded that will restore all the quarantined files back to the normal locations. Unfortunately for many people this patch won't work as they are unable to start Windows in order to run this program. If this is the case, then BitDefender is suggesting that you first start Windows using your Windows CD and perform a repair on their Windows directory. The Windows repair process will replace all of the missing Windows system files that are missing so that you can then start Windows. Once Windows is started they want you to run the patch to restore any quarantined files. For more detailed information about this procedure, please see this knowledgebase article on the procedure.
BitDefender has also stated that malware developers are already starting to take advantage of this chaos. These malware writers are creating sites that masquerade as legitimate ones that offer solutions with their own patches. When you visit these sites, though, they will instead show pop-ups or fake online scanners that state you are infected and try to push rogue software on you. An example that was found with the search keyword bitdefender FakeAlert.5 can be seen below.