I've had this problem quite a lot on V6.
Sometimes, when a wait timer is set on multiple frames, even though the number of ms. are the same, the actual wait time is vastly different. A three frame example - with, let's say, 6000 as the wait timer for both transitions - doesn't always lead to the same time being delayed between the frames. Sometimes, though, it does work as it should.
I haven't seen anybody else notice this, so it might not be an issue with the editor at all.