Oh, hey Jimmy! I actually kind of guessed this was you before. Posting about VE Pro combined with that nick & picture, gave it away!
Anyway that’s good to know that it doesn’t happen with Logic. I guess an effective way to see whether it’s Cubase-related or not would be to test the VST version somewhere else, like Reaper. But in any case this same thing seems to happen on Windows as well, so it’s just the way it is at the moment.
I’ve simply started using a single session for every project, did two features so far with this method and no issues (knocking on wood)… It’s a bit of a hassle shuffling things with Process Bars and Time Warp, but it still seems like less trouble than loading different sessions and matching tracks, routings etc. across them. Plus you get a nice full tempo map to import to Pro Tools for the scoring mixer, nice to have the grid line up still in the mix phase as well.
Have to be very careful though to back everything up as often as possible, keeping all the past versions, both in the Cubase Project and XML format. Session corruption with the single session solution and no past versions would be a pretty sure way to induce a drinking problem!