Ok, so the files are there, I don't have a virus. It is using the %systemroot% variable, and when I do a start->run->cmd %systemroot% it does bring up c:\windows like it should. In my autoexec.bat it is appending one line to the path. Hrmm... as I am messing with this my path gets reset every time I either open or close the command window. If I set the path it all works... but reopen the window and the old path statement is back.