Years ago with my trusty Sonar 4 my win XP computer I experienced a similar problem. That PC had two hard drives installed, so when I moved a song project onto the C drive it sputtered in a different manner
I was stumped, tried defrag and other utilities.
What I finally noticed was if I attempted to process a file through T Racks, the progress bar stumbled,
It was both hard drives that went crappy, they worked, but there write speed was not up to par
Lesson learned after that, in the drive bay, space the drives apart, if possible