Hey Chilly, sorry for the long delays in responding, Ive been busy. I am going to instruct you on running a few diagnostic tools and utilities to try and determine the source of the problem. I am going to break it down into steps and separate the posts so you don't become overwhelmed or confused. (I'm not saying you would get confused, I just find its easier to process little bits of information at a time, besides these steps are really time consuming.)
1) Download a program called "Hijack This" you can get it from here: HijackThis - Trend Micro USA
2) run HJT (Hijack This) on the computer with the problems and after running it you should get some sort of text file. Attach that text file to your next post.
3) also, just so we don't overlook anything, go into the command prompt and run Checkdisk (with the /f parameter) You will want to put a few hours aside so it can run. You can find out how to do run Chkdsk here: PC Jargon » CheckDisk (chkdsk.exe)
4) After running checkdisk you should find a text file containing the results. Attach that to your post as well.