I doubt that its the GPU if you are still able to interact with a program during an episode. First, I'm going to assume that you used the same ram with the new mobo? If so I would test that.. But again I some how suspect that this isn't caused by a hardware issue as much as I would say that its a software issue. Have you tried running a /chkdsk r ?
Running /chkdsk r:
Manual steps to run Chkdsk at the command prompt
1. Click Start, and then enter cmd in the search bar and hit enter
2. Use this following procedure:
• Type /chkdsk r (notice space between the k and r)
Note If one or more of the files on the hard disk are open, you will receive the following message:
Chkdsk cannot run because the volume is in use by another process. Would you like to schedule this volume to be checked the next time the system restarts? (Y/N)
Type Y, and then press ENTER to schedule the disk check, and then restart your computer to start the disk check.
Let me know how you do,