I thought I had this solved a long time ago, but I am having trouble.
 
1-Song with a couple of minor tempo changes (slow down and then go back to original tempo in one section, and then slow down at end)
2-After I edit in Melodyne, things sound fine.  When I bounce down (using "Bounce to Tracks"), the bounced vocal is out of sync with the track.
3-I thought the solution was to add Melodyne and--without transferring audio--open the Tempo window in Melodyme and play the song all the way through.
4-Then transfer and edit the audio and all would be well.  But I cannot get the bounce in sync.
5-The last time I tired just now, the bounced audio was about an 1/8 note ahead of the beat.
 
When I "teach" Melodyne the tempo by playing the song through, in the tempo window i select varying tempo--not constant tempo and not stretch audio.
 

Now the Melodyne track doesn't even play in sync.

if the bounce is different from the playback, that seems like a problem with how melodyne is working with sonar.
 
Are you using Sonar X1d?  The obvious suggestion would be to upgrade to an edition with ARA and see if that works. 
 
I remember having issues with melodyne and tempo changes before, but I can't remember exactly what the issues were.

I started another thread on this with different and addition information, but it seems to have been deleted.
 
As far as I can tell, the solution to this issue is *DO NOT* use Fast Bounce when bouncing to tracks.
 
I worked on a track this week-end and started completely from scratch on my Melodyne edits several times.  The bounces were all out of sync, with each vocal phrase farther behind the track than the previous one.
 
I tried turning off FAST BOUNCE and the result was perfectly in sync.
 
I need a few more trials before declaring victory, but this seems to be the solution.