Long/short rests seem to be working again.
I did see one strange case. If something is in the CT and the clock is used to advance the time. The effect can hit exactly zero and get "stuck" on the character. If I move the round forward by one, with the CT and then switch to the clock, it drops off as expected. Is there something I need to set to catch these or I have to at least use the CT for one of the rounds?
Thanks for the quick fix!