Unfortunately I can't offer a solution to your particular problem.
In my experience and according to what I've read in the forums, any VST or other program doing pitch shifting should be handled with utmost cautiousness. Maybe their task is of such nature that problems occur very easily.
My recommendation is to do the pitch shifting in portions so small, that you can finish what you're doing, and never need to leave an unfinished clip in (say, loaded in Melodyne) when saving. Also disable the pitch shifter before you close SONAR. When the pitch correction is done, bounce the track and delete the pitch shifter.
I have no idea what exactly caused the problems I experienced with Melodyne Plugin, so my being so carefull may be silly, but I've read many posts about similar problems on the forums. Following the procedure I described, Melodyne works great.