After correcting pitch for vocals using Melodyne region fx in sonar x3, when I bounce to clip, the audio 'clips' (the volume is increased significantly so the audio clip distorts).
 
The same thing happens in melodyne studio (standalone) but it gives the option when exporting 'the audio will clip, should melodyne readjust volumes to prevent clipping' which takes care of the problem.
 
Can anyone confirm this, and is there a solution?

I am wondering why volume is being shifted with pitch edits. Since it happens in stand alone mode as well, I would recommend contacting Ceremony directly. I have personally not seen this, and cannot think of a solution (or why).

I was wondering if you found out what is causing the problem.... I am having the same problem, but it takes place with plain bounce to clips, v-vocal, and melodyne, total pain in the arsssss! If I just select a clip, then turn it into a region fx, bam, 3 to 5 db increase, and when i bounce to clip again turning it back into a standard wav clip, bam, another 3 to 5 db increase.... if I just right click and choose bounce to clip a slip edit, again 3 to 5 db increase. THIS IS NOT A MELODYNE OR V-VOCAL PROBLEM!!!! I uninstalled all melodyne and v-vocal programs and it still does it when ever I bounce to clips a edited clip. Very frustrating and I have not heard anything from cakewalk support, I even sent them before and after pictures.... still waiting. This seems to be the only problem I have encountered with X3.... I can deal with crashes, I push this program hard, and crashes are typical when you have deadlines and you are beating the hell out of the program, but this is a major issue when pitch correction is desperately needed. I can't believe that no one else except a couple of people are having a problem with this.... you can visually see this ridiculous increase in amplitude. Hopefully cakewalk support is on it. 

Is there another effect inserted on that track/clip? Do you have a compressor with makeup gain, or some other effect that increases gain that is "applied twice", once when the clip is bounced and again on the track/clip itself, when played back after having the processing applied?