So, it would appear that this issue is universal.
 
If you are using Melodyne with ARA in Sonar, be careful to check that any notes quantised with the Quantise Macro, or manually aligned with Melodyne's grid are actually "in time" with your project.
 
The discrepancy is cumulative and will appear  greater with each measure.  Nothing will appear visually untoward  in Sonar unless you bounce to clip, so you will have to listen for it.
 
It is also tempo dependent.

Thanks for the update and feedback, hopefully they'll get this corrected soon.
 
I haven't used the quantise function, I'm doing manual work so I haven't experienced the degree of frustration others probably have.  I've pretty much been splitting my tracks into short clip segments (vocal comp'ing) - I align my Now Time marker in Sonar where I want it, and use that as my reference in the Melodyne editor.  The time markers in Melodyne don't align, but it allows me to tighten vocals together pretty readily.

I'm also seeing this regularly in Melodyne Editor. I take it there's no solution at the moment?

I have reported this, and according to Cake there is a rounding error in an algorithm that is causing it, and it is now with the development team.

It appears worse at certain tempos, and increases the further you go into the project. Very few people seem to have noticed it yet, which is surprising.

Let's hope it's fixed in the next update.

Thanks for the update ... and for blazing the trail on this.
It's good to know they're working on it. I guess in the meantime, we just use Audiosnap for timing corrections.

Not sure if this is related, but I noticed if I have multiple clips with Melodyne (Editor ver.)  as region fx, and I have more than one melodyne in the dock, editing in melodyne becomes erratic. Keeping only one  editor open  at a time has kept this from happening again.
 
Another issue I've noticed is that melodyne does get out of sync with sonar, but when I  undock and redock the editor, that seems to "fix" it.
 
Again not sure if these are the same issues. Both of these happen when the editor is docked.

groovey1
Thanks for the update ... and for blazing the trail on this.
It's good to know they're working on it. I guess in the meantime, we just use Audiosnap for timing corrections.

We can still use Melodyne for timing corrections, as MorganT pointed out in post #22. It's a workaround, but it works. It means the quantise macro is no use, but we can correct individual "notes".

Thank you for your thanks. :-).

I don't know if this is related to the Melodyne problem, but I've had the same problem when using Audio Snap. After using Audio Snap  & bounce-to-clips on a conga track, the wave form does not line up with what I'm hearing. It's fine for most of the track, but about two thirds of the way through the wave froms fall noticeably behind the audio. The track sounds fine, but the wave form is about an eighth of a measure behind, and stays out of sync for the rest of the track. Melodyne has not been used on this track, only Audio Snap.

I've not seen that, I'll have a look later, if I get a chance.

Don't think it is related to the Melodyne/ARA issue, though, but I'll do some digging.

i am experiencing this problem right now, with only one region fx clip in existence at once.  i have the newest version of the editor & X3d x64.