Well, I just spent over an hour on the phone with Waves, and since the problem only happens after I make edits or changes to other tracks within a file, Waves seems to think (and I agree) that the problem is that something is getting corrupted within the session in SONAR that is affecting how the Waves plugins behave. I can run these plug-ins without issues for days and all of a sudden I make a change to a track that doesn't even have a Waves plugin and then I start getting these audio glitches. It is a strange issue and I hope that someone from Cakewalk reads this and can either PM me or post here and see what we can do.

If you don't have any Waves plugins in the project does this still happen? Does it happen with other plugins? Someone from Cake will need to chime in on this one. You can try opening a case but you will have a long wait for help. 

Nope. This is Waves/SONAR specific. This is what Waves tech support wrote: "As we discussed, it seems that the issue occurs due to a corrupted Sonar session, as your previous edit, plus 18 drum tracks and more CPU intensive, works perfectly."

Bump!