Stretch it out so that you end up with the correct last frame before the glitch. Set an Out point on that last frame and Export out a new clip for continued editing.
Try transcoding the clip to a production codec, then perform your speed effect. Holds up better? Let us know.
Thanks for the quick help everyone!
I actually solved it similar to Kevin's idea -- My project was 4 layers and only one had the rate stretch/optical flow applied. I just made an export of just the layer with the slow-mo effects as a QT Animation w/alpha, then brought it back into the project so I no longer needed the speed effects while creating the loop. Added back the other layers and it's looking great.
Cool! Thanks for reporting back.