I haven't done any testing against VideoClock yet. So many things that interact, so little time. It'll definitely be on my list to checkout eventually. If you or others can confirm its fine without, and using it causes issues, that would be helpful.
Do you get audio or video issues when this happens? The frame time log didn't include anything meaningful, just one or two drops and one repeat or such, but nothing that would tell me there was a significant issue.
Also how long is "a while" to trigger this?
Are you playing on a perfectly matched refresh rate, or a mismatch?