I get problems like this all the god damn time using Massive. Crap like my patches changing their sound slightly every 2 bars, patches sounding completely different everytime I open certain projects, random volume changes and sub problems like you've got. I've gone through all the settings, routing, voicing, you name it. The only thing I've found is that it's most likely to do with the oscillators. Certain ones like Maygr have a tendency to be dicks and do random, annoying shit to piss you off.
If one of your basses is giving you trouble, I suggest you bounce it down to WAV. so there can't be any fluctuations in it's sound. Saves on CPU as well.
If anyone knows what's really causing this problem, please elaborate. I'd love to know how to stop this shit. Really, please tell me.