Mine's not as severe, but it's impossible so far to determine a pattern as to when it happens. I can switch to a new patch, then come back to the Pro-3 in a few minutes to see the window now shows the VCA info with the VCA Env Amt tab active. I believe it's also clobbering values, but no smoking gun yet.
ADDED: Come to think of it, from day one, I'd leave my favorite patch on there, then turn back to the Pro-3 an hour or more later to find the sound clamped down and not giving off much sound at all. Switching away and switching back always fixed it, and I'd always thought it was some unpleasant quirk of my unit when it was left idling too long, but now it seems like it may be this same problem where the VCA envelope settings get changed. I never checked to see exactly what had been changed, just always switching away and switching back. If I'd noticed it was part of a larger pattern, it could have been taken care of within the 30-day return period, but now I'm stuck, possibly for a big expense because I have to ship overseas for service.