Welcome to Windrivers Legalegl!
Boot to command line mode or use a bootdiskette and check in win.ini for anything against the run or load lines, if there is put a ; at the start of the line, to stop it from executing. Now go to system.ini and look for shell= - it should be shell=explorer.exe If it says anything else, put a ; at the start of the line and underneath type in shell=explorer.exe
I would also suggest putting the drive in a machine with uptodate antivirus and running a thorough check. I would also run
spybot while its in there (don't forget to immediately update spybot after installation)