Anderton
Everything worked as expected. Because I can't get it to misbehave, I can't tell you how to avoid having it misbehave.
The only suggestions I have are:
- Try changing Melodyne to the Percussion algorithm.
- I noticed as it was doing its thing that the first screen shows "mixing down audio." Maybe try using half of the stereo pair?
Thanks a lot for trying, much appreciated. I do wonder whether it makes a difference what melodyne version is installed or is this drag to timeline fully integrated into Sonar so that it also works without any Melodyne installed?
I stayed at Melodyne 2.1.2 and so far have not bothered to upgrade as version 2 does the job.
Anderton
Next bug: if you make the mistake to drag the "track waveform preview" which is the combined display of various comped takes of e.g. 4 takes, the ARA analysis is performed on every (!) take and not just the one that is not muted. you can actually watch it cycle through all takes, bouncing muted takes internally to silence and then trying to ARA analyse it ...
This probably isn't a bug. Remember that although Melodyne is integrated with SONAR via ARA, it is not part of SONAR. When you drag the parent track, you're dragging all the Take Lanes. Melodyne probably doesn't know which ones are muted and which ones aren't. This would need to be a feature request, but for now the solution is don't make the mistake of dragging a parent track with muted comp tracks into the timeline. 
Now being aware of it, I can flatten comp and drag that to the timeline ... or bounce to new track for safety ... somehow it seemed logical to me that Sonar should only pass what's audible for analysis ...