The sync problem is caused by the sound loop being unbalanced, that means when drums are muted it will on average run slightly slower than normal. But you're in luck (somewhat) - I fixed this issue in trunk today, so the upcoming release will have stable timing unless drum modes 2x..4x are used.
It'll still be a while before the next version is officially released, but if you don't want to wait you can already grab the latest beta from github. Note that some fx commands are changed in the beta, see /docs on github for details.