Worrying changes in audio tracks playback where tempo changes involved

Here's the project: a half dozen MIDI tracks playing back via a drum machine and my Roland Fantom X6.  There are occasional tempo changes in the song, e.g. going in and out of choruses and to make a slowed ending.
 
I had vocalist sing a vocal track the other day and all was ok on the day playback-wise.  Her vocal track was recorded along with the MIDI tracks running, tempo changes included.  Today I've done some tweaking of the vocal track in Melodyne and bounced that to a new track, muting the original.
 
Here's the problem.  When I play the song through, the vocal track sometimes goes out of sync with the others.  If I stop and restart, things sometimes sync up.  In other words the going out of sync is totally random.  I've never experienced this before and always done projects with MIDI and audio tracks together.  Has anyone any idea what could be causing this?  Have I perhaps failed to make a setting somewhere?
      

Thanks CJ.  I've always done fast bounce for this, but I'll try real time and see if that's better.

John