Try using your mouse to hit the "stop" button instead of the "O" on the numeric keypad.
I was experiencing the same thing on my HD system... only a few digitized files would get through and then the next one would be corrupted. It was M100 tech support who suggested mousing and clicking the "stop" button instead of "O". That fixed the problem. It's not as handy and quick, but I've not had one failed digitizing situation since. Learn to keep the cursor over the "stop" button, and click the mouse when needed.