whoa, interesting story there. Not too long ago I was experience a problem kind of like yours, one day my computer was acting up on me and disconnecting me and also rebooting. I figured it had to be a virus, norton didnt seem to detect anything, neither did McAfee, so I left it alone. A few days later it was even worse.
I decided to figure out the problem: I looked over my hard drive and found some suspicious files that I never had, I pressed ctrl+alt+del and checked what programs were currently running, it showed a WININIT.sys and WININIT.exe (took up lots of RAM), I looked for the file but couldnt just delete it because I knew the trojan was all over my hard drive. I did a port scan and found my port 137, 138 open. This port is usually never open, after doing some research, I figured out I had this trojan called WININIT (a.k.a MS3016.exe). The article said it opens up your port 137 and it makes it available to anyone.
So I looked at the registry files and found them clean, kinda like you did, so I really just restored my PC. A week later I found the computer still had the virus (stupid me  ) so the day later I just restored again and installed XP which the virus cant run in. I looked for the virus using XP's advanced searching, found it, replaced it. And now my computer is working fine. up to the moment at least.
thats what I get for downloading my warez, I stopped though 
still have port scanners and stuff though and I got rid of norton and mcafee, too many errors and it doesnt detect crap.
I just manually detect trojans now and do port scans and registry checks every once in a while
-Josh 
|