I've found Melodyne to be quite buggy since it was first bundled with Sonar (was it X3 when it first appeared?) and I ended up deleting all .dll and .vst instances of Melodyne from my system except for the .vst3 file and thus far I've been okay. Using the RegionFX especially caused issues. Have you tried putting Melodyne in the FX bin, opening it, and capturing/transferring the content in real time? Certainly not as efficient but at least for me that tended to be less glitchy than using RegionFX/ARA.