IE and Windows Explorer Slow

I got hit by a virus that disabled my virus and malware software. I had to shut down to stop it. I then installed fresh versions of AVG, Adaware and Spybot, and found 550 malware and 9 virus entries were made/installed. I successfully removed everything (that I could find with multiple scans, reboots,scans,etc). Now IE, My Computer, Windows Explorer and Control Panel each take a full minute or more to load. Once they load, they run normal speed. I’ve intalled Firefox to replace IE and it works fine, and I’ve installed 2xExplorer to replace Windows Explorer and it works fine too.
I need to resolve this problem, at least so I can get to My Computer and Control Panel.

Short of a Format/Fresh Install of everything, where can I look to find my problem?

Thanks,
Sup