Just went to the melodyne forum (man, there a lot of unhappy Sonar users!) and the looping issue is known. One guy had a good workaround, though.

You can set sonar to jump back to the starting point every time you stop (this seems to be my default behavior). So just start wherever you want and as soon as it gets to your desired ending loop point -- just stop sonar and the cursor will jump back. It is manual looping, but it should work OK. The main reason is that Melodyne takes the track that you have the plugin on and creates its own little universe to run it in (it has to analyze the entire track in melodyne to determine pitches and display the blobs) Based on what melodyne has to do, I can see how getting the loop to be in synch would be difficult.

I'll have to give the work around a try.

Now at bandcamp: Crows Say Vee-Eh @ bandcamp or soundcloud: Kevin @ soundcloud