Sometimes, seemingly randomly, when I create a Melodyne clip and move some notes around, I get the original audio playing in the background, creating a chorus-like effect because I mostly do small pitch correction. I haven't been able to figure out what causes it, but once the effect appears, I can't create any Melodyne clip without it happening until I close the project and reopen it. Has anybody had this and perhaps found a permanent solution?

The chorusy effect you hear is called 'Phase' or 'Phasing'. I have not run into hat and i use Melodyne frequently, but its caused by the original clip being played while the Melodyne effected clip being played at the same time.
 
Make sure input echo is not enabled. This may be your problem.
Also, what version of sonar are you using?
 
CJ

I don't think it's phasing since it's clearly two different pitches, and not a minute time (phase) difference. In fact, any blobs I haven't moved play back phase accurately with the original audio. I figured it was the original clip being being played, but unlike in older Sonar versions with V-Vocal there is no actual original clip "behind" the Melodyned one, otherwise I'd start looking there.
 
It's not input echo. I'm on X3e right now but it has happened as far back as at least X3c.
 
 

The 2 different pitches is prob the original and the one being edited. I have the Editor version of Melodyne, so i do not really know if Melodyne one behaves like the Editor version. It should though.
When you move a blob, you need to play it from inside melodyne, (IIRC) or you need to render it, when moving blobs.
 
 

I also have Editor. I agree it sounds exactly like the original and the edited one, I just can't find where the original is playing from. In previous Sonar versions there would be a muted clip behind the VVocal one, that's not the case anymore, at least if there is one it's not user accessible anymore.

Are you using "Region FX" to create the Melodyne clip?

Do you have 2 tracks with the same audio.... cloned or copied?
 
Normally when ME is active, you will only hear the ME output and the original track is not audible.
 
I don't think I have ever heard what you are describing in all the years I have used ME for editing with just one track.... I have used the clone a track method when working on vocal tracks that were sent by other people...as a safety precaution and forgot to mute the original....and that happened.

Using region fx. No cloned tracks. I'm doing everything the normal way. I have never had this happen until X3 and ARA either.