I recognized the following now time mismatch between Melodyne (Assistant) and CbB:
Melodyne in clip or track mode:
If you use certain fx plugins in the project, e.g. TS-64 Transient Shaper and/or LP MB the now time cursor in Melodyne will lose synchronisation with the audio playback and with the now time cursor in CbB. In my case Melodyne is ahead e.g. half of a measure (see attachment). If you switch off those plugins synchronisation is OK again.
Melodyne in note assignment mode:
Measure 1 in Melodyne starts at the beginning of the Melodyne clip. Thus if the clip starts not at measure 1 but later, you can have several measures time difference between Melodyne and CbB. A workaround for this problem is to move the beginning of the clip to measure 1 and afterwards you make a Melodyne region fx.