Hmm.. more information is really needed here..
- Most importantly, what did you do to the file in Melodyne?
- Did you actually export an audio file to a stand-alone version of Melodyne and back? If so, why not use the Melodyne plug-in within Ableton, which should be easier?
If you did export/re-import the audio, I'd try doing the same operation[s] in the Melodyne plug-in within Ableton and see if that works properly.
You asked "is it something in melodyne that causes the changes" ..?? As you know Melodyne is all about time-shifting and pitch-shifting, so of course the file will be changed.. For example, if you, say, quantized in Melodyne, and Melodyne's tempo analysis did not match the actual tempo of the Ableton session, then I could see how that might result in a loss of sync. That's why you'd need to be specific about what you did with the audio in Melodyne. It's also why I'd suggest working with the plug-in within Live, where sync should be automatically maintained.
I've attached a Melodyne course [above] -- maybe something in there will be helpful [check out video #2 in particular]..