I have X1 with Melodyne Editor.  In order to bounce the track and have the effect in the new track, the track must be selected.
 
I almost never use Bounce to Track anymore when I work with melodyne.   I simply use Process And Apply audio fx to the existing track. 
 
The reason is, since I have used ME to fix the vocal track, I obviously do not want or need the old non-fixed vocal so.... why not simply do the "apply FX" to the audio right where it is?  Works like a charm but also.... that clip or track MUST be selected to apply that FX to the audio in the track.

I tried Herb's suggestion and had the same problem: the resulting audio did NOT have the Melodyne edits applied.  What is worse, the level of the wave was way down from the original.
 
I have the track in POST mode because otherwise ProChannel will not have any effect on the transferred Melodyne audio.  Of course, I can turn this off while bouncing if that is the problem.
 
I would really appreciate it if someone can tell me why Bouncing a track with Melodyne results in the original, unedited audio.  Thanks.

Konrad, is this on X1d?
 
I thought I could help but might have to punt. I opened X1d and Melodyne only shows up for 32bit (64 bit isn't listed anywhere), and has to be inserted as a plug-in. Without ARA, there is a "transfer" button in the upper left, which imports the audio clip into it. I *believe* once edited, that same transfer has to be done to re-write the audio for SONAR to use. This is essentially the same as processing the effect in place as mentioned above. Definitely read the manual on the transfer button if you *are* using X1d. This is my first time experimenting with it outside of ARA mode :(
 
Edit: 64-bit is under Rewire, need to tinker some more... okay... definite punt here, it is giving me more grief than answers. Sorry...

Thanks for trying.  I am on X1d and everything is 64-bit except the Fantom built into the VS-700 studio.
 
I have used Meldoyne extensively for quite some time and cannot figure out why it won't bounce or process right.
 
For now, I can export audio OK but it makes me nervous to have a record with 15+ tracks of Melodyne.  I would fell better if I had a copy with the edit vocals somehow saved just as wavs.  Ideally, I would keep a copy of the project with Melodyne, but have another bounced version without all the Melodyne instances so 1-there would be less CPU load, 2-less danger of losing the edits, and 3-ability to export to other DAWs or editors, should that be needed at some point.
 
Transfer definitely is how you bring audio in.  I don't think you get it out that way: hitting transfer again overwrites your edits and brings in a fresh copy of the original audio.
 
 

I received this answer on the Melodyne Forum:
 
"If you are trying to use Fast Bounce w/Melodyne in Sonar X1d it will not work, you have to use Realtime.  This was fixed in X2 and later.  I can't remember if X1c & prior worked or not but I think one of the earlier versions still worked."
 
I will let you know if resetting the Bounce options works.