Is your Melodyne the latest version? Are you using the Melodyne as a Plugin or as stand-alone?
I use Melodyne (latest) with Cubase 5 as a plugin and experience no problems. I'm on a Mac.
Jeff

I'm not a Cubase guy and I don't own Melodyne so I'm at a bit of a loss if all your other plugs work correctly. Is there a spot somewhere to assign timecode to the tracks? This would keep them in sync. Also, as I understand it, Melodyne will stretch the time as one of it's processes too so perhaps there is some automation within Melodyne at work.

I own Melodyne, but not Cubase so I have no experience with it there. This is off Celemony's web site if it helps at all (although you may have already tried it or it has nothing to do with your problem)...

[Sync offset by cycle length]
Activating the cycle in Cubase or Nuendo, but starting the playback at any position behind the cycle will offset Melodyne.
Workaround: when you want to play back at some later point in the song, turn cycle off in Cubase/Nuendo.

As well, one guy set up Melodyne to "transfer" to a separate hard drive than Cubase tracks to. Not sure what that would do. Maybe relieve one HD from working too hard.

Did you set up the plug-in to the correct tempo prior to the transfer? Is it possible that Melodyne didn't grab the correct info from the DAW with respect to the project tempo if you didn't?

Might have automatically time corrected. I believe once you've closed your project Melodyne removes all undo history whereas the stand alone version does not so it can't be undone. Try removing the plug-in and re-inserting it on the channel strip.

Is Melodyne the very first insert on the channel strip?

Melodyne's user manual (pages 114-117 of the "Assistant" version) may be of help too. Talks about tempo changes and how to match them with the DAW.
celemony_ :: Manuals

Just some thoughts.

It seems to be a common problem on many PC/MAC systems.

I'm using Melodyne 3.1, via the Bridge VST plugin. Also tried ReWire but can't get anything to record in Melodyne that way.

I have that problem with Nuendo 3.0. The problem only comes up after I close and reopen the song. So I typically transfer to melodyne fix what I want, then export just that track with the fixes to an audio file, then replace the original track in the song. IT's PITA, but it works 100% of the time. I would to hear more on this topic.

Link555, post: 359412 wrote: ... fix what I want, then export just that track with the fixes to an audio file, then replace the original track in the song. ...

Tried that, still out of sync.

Then Melodyne is actually adjusting the time somewhere. Otherwise the file length would be the same.

My song starts at 160 BPM and accelerates to 162 by the end. Wanted to give it "energy". Artistic decision, done with Tempo track in Cubase.

So I told all this to Melodyne, too. Variable tempo editing, markers, etc. Still no avail.

It must be me, I might be ignorant of this since it is new to me.

Tried that, still out of sync.

Do you still have melodyne on the tracks inserts?

OK, so I went to a different song with a straight tempo. I syncs perfectly! Ok, so I'm a knucklehead now.

Yes, the bridges are still on my inserts. Anybody got a quick clue on setting up an accelerating tempo? I thought I did it right but I guess not.

Thanks!