New user of Melodyne Essential, Sonar X3 Studio.  Hp 6200 quad core processor, 8GB ram, Win 7 Pro 64.  
 
I used Melodyne Essential to process the Bass track for timing errors.  When I play the whole song back, everything plays fine, all 12 or so tracks, but when I try to record a new guitar track, the Melodyne'd bass track plays back out of sync while doing the recording.  If I play a different bass track that doesn't have Melodyne processing, it all plays fine during recording.  I also had something similar happen with the lead vocal track, which was also processed with Melodyne. 
 
What is the problem here ?
 
I got an error message every time I used to open Melodyne, saying my buffers need to be 1024 .  In my Sonar Studio X3 under Audio, Preferences, Sync and Caching,  File System,   I can see the Playback I/O buffer size is 1024kb, and the Record I/O Buffer Size is 1024kb.  Is this the correct buffer size parameter I need to be looking at ?  If so, what is the problem ? Do I have to enable read and write caching ?
 
Thanks much,

I am having this exact same problem.  I thought it was something to do with the audio interface.  I just bought Sonar X3 Producer, and PresSonus Audiobox 1818VSL at the same time.  It took me a month to figure out why my vocal track was out of sync.  I've been searching all kinds of forums thinking it was a problem with the Audiobox working with Sonar.  I disabled Melodyne, and everything went to normal. 
 
Does anyone have a fix to this problem?

Chevy
New user of Melodyne Essential, Sonar X3 Studio.  Hp 6200 quad core processor, 8GB ram, Win 7 Pro 64.  

I used Melodyne Essential to process the Bass track for timing errors.  When I play the whole song back, everything plays fine, all 12 or so tracks, but when I try to record a new guitar track, the Melodyne'd bass track plays back out of sync while doing the recording.  If I play a different bass track that doesn't have Melodyne processing, it all plays fine during recording.  I also had something similar happen with the lead vocal track, which was also processed with Melodyne. 

What is the problem here ?

I got an error message every time I used to open Melodyne, saying my buffers need to be 1024 .  In my Sonar Studio X3 under Audio, Preferences, Sync and Caching,  File System,   I can see the Playback I/O buffer size is 1024kb, and the Record I/O Buffer Size is 1024kb.  Is this the correct buffer size parameter I need to be looking at ?  If so, what is the problem ? Do I have to enable read and write caching ?

Thanks much,

You need to raise your soundcard audio buffers to 1024, that may help 
Also have you tried bouncing to clip once you have finished editing? (right click on clip to select)
 

Thanks Chevy,
The buffers were set to 1024, and was still out.  I ended up bouncing to clip, and that resolved it.  I'm thinking that having Melodyne as an active plug in shouldnt cause these problems.  Wondering if you can keep the plug-in on and active without these problems, in case you want to make more changes in Melodyne.

It may be a plugin thats causing it. Try bypassing all FX in control bar to check

I don't even recall what caused the problem for me anymore...!!!!   aaargh. sorry. But I did have 3 issues that were coincident at the time: 1) my Scarlett 2i2 interface buffers were not set to 1024, and there was no way to specify 1024 that I could see...   called up Focusrite, they got me to install a new driver, and voila !   Now I have a proper software control panel for the 2i2.  2)  a bass line I recorded for some reason had TAKE LANES implemented. I don't recall optioning the Take Lanes recording option, but as soon as I got rid of that feature, on that one track, Melodyne behaved. There were several very weird problems that were introduced to this project due to my using Take Lanes on that one track. Celemony support themselves said they weren't familiar with Take Lanes... oh, and 3) I started a new project, copying over most of the tracks.  
So, somewhere in around all this confusion, the out-of-sync problem disappeared.  
Hope this helps.