Looks like those are something different. I think what's happening (when it happens: it's infrequent and not repeatable) is that timing is off when I'm working, but then is rendered the way it should be. I'm thinking this because when I've noticed this, it will sound in sync but visually the waveforms won't be aligned. The render is happening in the "correct" timing, but listening in Reaper before render is not. Whenever this happens, restarting Reaper had brought it back to proper operation. I guess the answer is that when it seems to take misaligning the files by visual cues to have the audio sound in sync, the glitch is probably occurring, and I need to restart and then try aligning the files again.