If I may be so bold, I think I can contribute a couple of useful things to this discussion:
1) Celemony only makes one Melodyne installer and, in theory, it's the same one that's included in the Sonar X3d update. It's the specific authorization process (and serial number, I suspect) that decides which version is activated (Essential, Editor, whatever). I read this recently in some Melodyne documentation.
2) Anytime you make changes to a track/clip with Melodyne, V-Vocal, or AudioSnap, bounce the track before doing any other timing/pitch corrections/modifications. For some reason, doing any other adjustments with another one of these three tools just isn't working well right now. Bouncing in between, although it's time-consuming, does work.
 
I hope that helps keep you from getting bogged down while the programmers are working their magic.
 
[EDITED for clarity]

Dear, rontarrant I have only one thing to discuss: I had a very very good and important thing for me in X3C, which I do not have in X3D. I know all about your paragraph 1 and 2. :-(
 
Alex, this message I received 26.12.2013  
Hello Grivanov Eugene,

Thank you for contacting Cakewalk Technical Support. We have received your question and will reply as soon as possible.

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Best Regards,
Cakewalk Technical Support
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Note: This is an automated message. A Technical Support Representative will reply to you as soon as possible. Thank you for your patience in the meantime.  
 

So just finished the Groove3 tutorial for Melodyne so I figured I'd get around to this...
 
STEPS
1) Create audio track.
2) Add audio, grab a vocal track from somewhere (say).
3) Create RegionFX -> Melodyne
4) Treat all the clips in Melodyne (use the macro).
5) Create new audio track
6) CTRL + SHIFT + Drag clips to a new audio track.

EXPECTED
Two identical Region FX Cloned Tracks, if you play back SOLO'd there will be no phasing.

ACTUAL
Two Region FX Tracks without the Melodyne Edits you made in (4), phasing like the moon.

WORKAROUND
Clone track.
 
So I can reproduce this (CWBRN-23145)
 
Cheers... 

Alex, you are the Best !!!

I'll let you know if Cake confirms this. Cheers Eugene... :)

This sounds like an problem with the ARA integration rather than Melodyne itself. I've experienced some serious ARA related problems which I've bugged up, mainly related to moving Melodyne clips around. In one case I completely lost the audio in a clip when I moved it. 

Yes exactly. Bet its the same with vvocal but haven't tested...

The manual lists these:
Region FX clip restrictions
The following editing functions are disabled for Region FX clips:
• Clip automation.
• Copy/paste for a time selection that contains a Region FX.
• Split clip.
• Slip-stretch clip when the Follow Host Tempo option is enabled.
• Groove Clip looping.
• AudioSnap.
 
I wonder if the 2nd item prohibits copying exactly a region.
 
For the similar clone issue, Melodyne misbehaves, but not V-Vocal.

bvideo
The manual lists these:
Region FX clip restrictions
The following editing functions are disabled for Region FX clips:
• Clip automation.
• Copy/paste for a time selection that contains a Region FX.
• Split clip.
• Slip-stretch clip when the Follow Host Tempo option is enabled.
• Groove Clip looping.
• AudioSnap.
 
I wonder if the 2nd item prohibits copying exactly a region.
 

I guess so. It does say "disabled for Region FX Clips", and copying a Region FX Clip is "a time selection that includes a Region FX".

CWBRN-23145 now confirmed by Cakewalk.