I've never seen this problem, but if I did, this is how I'd proceed...
1. Close the project without saving.
2. Reload the project, perform the exact same procedure again and see if the problem re-occurs.
3a. If it does - and it probably will - then yay! the problem is data-specific, AND you have a repeatable test case for Cakewalk to step through.
3b. If it doesn't - and that's far less likely - then it's intermittent, and that means you either have a plugin that performs some kind of random modulation, or it's hardware.