Long time Sonar user, new to X3 and Melodyne, X3D 32-bit update.
 
Using Melodyne to pitch correct a vocal - I add the region FX for Melodyne, and in spite of reading the Melodyne manual it's not clear to me what actually happens.
 
1. If I manually move notes to correct them, then on playback I hear chorusing on the vocals. My guess is that playback is playing the original untuned vocal at the same time as the pitch-corrected version, hence the chorus effect. Even on bounce-to-clip the resulting playback is chorused. We're talking about a 50 cent correction here, and I'm baffled why I can't just get a corrected pitch as in previous versions with V-Vocal that just worked.
 
2. It's not clear to me what exactly happens when the region FX for Melodyne is added. Does it correct the pitch then, automatically? What exactly needs to be done? I ask because the Melodyne help shows screen shots that do not exactly seem to fit what I see. Then there's Sonar docs that says "Region FX and there you go" and there are Melodyne docs that say "just do this" but there seems to be a gap in the integration docs about how it really works.
 
Being new to Melodyne in Sonar there's probably something obvious I've missed, but I've been on Sonar since version 3 and I've never come across anything quite so opaque as this.

I'll be following this as I'm in the exact same boat as you. I played around for an hour and gave up, It's a shame when that happens, I am usually pretty quick on the uptake. I abandon software if it has a illogical interface pretty quickly and never return. 
Antares auto tune and V Vocal seemed to work without even reading the manual.. 
But Melodyn is the most popular so I guess well just have to see what it is we're missing. 

I don't know about the chorusing, that has never happened to me. Are you sure you don't have a double clip somewhere?
As for how it works, it is manual pitch correction just like V-Vocal. You slap it on as a Region FX, its window opens, and then you get to manually correct notes (or select all and use the "correct pitch" for instance, which I wouldn't recommend).

1. I think you are correct that you are probably hearing the original track plus the modified track and the two together are causing the 'Chorusing'. So, I would start by doing a few tests to try to determine where the original track is coming from.

• It could be that you have microphone bleed where the vocal is loud enough to be picked up in the drum mics or guitar mics and that you are modifying the vocal track without modifying the other tracks. That would do it. From your post, I'm guessing this is not the problem. 
• Is it possible that you have multiple lanes playing back at the same time? Lanes can still be minorly buggy imho. I've seen some goofy stuff I couldn't explain. You might try tracking your clip you want to use Melodyne on to it's own track. This will ensure that no other clips are unmuted concurrently.
• Do you have the track Solo'd when you hear it? That's a good way to be sure the problem is coming from that one track.
• Are you using Melodyne Editor edition? If you are, and if you are using the Polyphonic editing algorithm, then it may be that your aren't successfully capturing all the overtones of what you want to modify.

2. When Region FX are added, Melodyne samples the audio to generate the blobs that you can edit. It's measuring timing and pitch of the audio. It's also assessing the audio to see whether the Melodic, Percussive or Polyphonic algorithm is most likely to be useful. The scale detective feature should also attempt to identify the key of the music.
 
At this time, it is NOT

• modifying the pitch of audio
• modifying the timing of audio
• modifying Formants
• modifying the amplitude

If you just highlight a track and press ctrl+m to create the Melodyne Clip, after creation, it should sound identical to before creation.

I know it's not bleed or anything like that because it appears *only* in the regions that I'm tuning. And I'm definitely solo'd.
 
The suggestion about a double clip somewhere might be what's going on. The vocal track was sent to me to add into a project, and so I imported the WAV file. It's possible (maybe even likely) that the track may have already have been tuned (not well, I might add) with a previous Sonar V-Vocal, so maybe there ARE double clips in the track. That's a good one to look at. I can also do my own vocals as a test - I was just a bit rushed yesterday and didn't have to time to do that.
 
 

Also make sure you have no hidden tracks.

Well in my case, it was a fresh inserted track, Record Bass,, I did re- record it a few times using "overdub" so I don't think there should be hidden layers. 
I had a few unwanted string snaps that peaked into digital overs. I'm away from home and don't have a compressor in the front as I normally do. 
I would normally tool copy to wave lab and kill the spike.. don't have that either, My only complaint about Sonar is it lacks any wave editing tools..Ya ya I could draw a volume envelope  but wait a minute What about Melodyne, me new toy. 
 
Basically I successfully deleted the offending note, it was visibly gone, but the pop was still there. Messed around for an hour and gave up. I guess I was possibly doing something it is not made to do, remove a noise. It just seemed that you could remove audio and it would still sound. 

Cactus, I would have split the clip around the bad note.

To get audio "into" melodyne you enable it to capture and then play through that section or the entire song. 
 
After it calculates and creates the blobs, you are ready to start working on the blobs.
 
At this point and before you do ANYTHING, click play and it should sound exactly like it did before you loaded Melodyne. Mute the track with melodyne and play..... you should NOT hear it. If you do you have a duplicate somewhere. Find it and remove or mute it. More than one time I have forgotten that I had a duplicate track that was not muted and yeah, it will make you pull your hair out.
 
When you are satisfied there are no other tracks interfering, begin the manipulation of the blobs manually as needed. On playback from this point forward you should only be hearing the changed blobs playing back. So the pitch that you fixed will be the one you hear, not the new and the old pitch together. Melodyne does not work like that as that would make little sense in playing the old and new together.
 
When I pitch fix the tracks with ME, I tend to solo the ME track and one acoustic guitar or piano track for a pitch reference point.
 
One thing I notice is that you do need to stop the playback and NOT jump using your mouse to click on the timeline. ME will not follow the click and will keep playing as if there was no click while Sonar will see the click and jump to that point. ME and the music will be out of sync, so it is important to stop playback to jump around, or back as the need arises.
 
There should not be artifacts from a 50 cent move so that should not be the cause of the phasey sound.
 
Every sound in that track should show up in ME as a blob. music as well as clicks and pops....and more actually. I see things in there that are overtones that ME picks up.
 
Yes.... be sure you're in the right mode.... Melodic for a mono instrument or voice.
 
There's a lot to this program..... more than I use. Watch the tutorial videos on the Celemony web page..... I learn something new every time I go there..... not that I use it all....

In X3, using ARA, you don't have to "transfer" a clip at all, this is confusing advice. Pressing CTRL+M on a selected clip or choosing Melodyne from the Region FX in the contextual menu automatically transfers the selected portion of audio to Melodyne and Melodyne will analyze it even before it opens its window for your edits.