If you are able to reproduce with the VST can you give a step by step instructions on how to get this to happen?
The quick answer is both are affected and is related to the buffering. There is also additional information I want to pass along about the au implementation and how to fix the modal and rack problems. It will be in PM because it's likely a dialogue about some of the internal mechanics (of an apple application) that doesn't need to be had here.
I was able to get the effect out of sync when changing the Internal Buffer size during playback. Stopping playback then restarting will fix the issue. I will report a bug to the developer for a possible fix.