I've also been fighting this problem for quite a while. I typically use flex time to correct timing issues, and then go to flex pitch. I always get garbled breaths and other areas as well, sounds really bad. So I created a new audio track, with no plug ins engaged, and copied my vocal track to the new dry track. Turned on flex pitch, did my edits, and no more issues. I previously had been doing my edits with a reverb plug in and EZMIX2 plug engaged, which flex pitch didn't like at all. Dry track seemed to cure it, sounding good now!