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I'm sure someone pointed this out or you may already be aware, but if you copy/pasted that warning, I'd say your faux window error is the actual trojan. When you're hitting yes, you're initializing the virus. Just sayin' since no one has mentioned it. The fact it's full of spelling and grammar errors...
This could be an extremely long shot, but if that warning is coming up on boot to the desktop, check this key in the registry:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon --> Look for 'Shell' on the right, and make sure the value in the Data column
only states 'explorer.exe' without the quotes.
Same key for XP and Vista.
If there's something other than explorer.exe, delete it. I used to get virus calls by the dozen a few years back with that one.
If that doesn't cut it, it's probably in your startup, services, or processes group. Unless you know what you're doing there, I'd go with what the other guys suggested. Online virus scanner, or FFR (FDisk (now Fucking, I guess, with FDisk falling into disuse on NTFS drives), Format, Reinstall).
Good luck.
As for the dude with the unreadable folder, it's a bad sector on the optical disk. Best chance of reading it is to reinstall the program used to burn the disk in the first place. Some proggies have proprietary burning tools like Roxio's old UDF piece of shit that can only be read by the original program on a certain OS (sometimes). Stupid upper and lowerfilters skin the optical drive drivers. Anyone remember the disappearing CD drive problem when XP was released? Roxio sucks ass.
Could be you encrypted the folder with Windows tools too, and you didn't back up the cipher key. Then you're fucked. No way of getting it back.