This is something I've noticed as someone who still uses Vue 6, but steps out into the new versions for their faster rendering capabilities. While it may not be all one thing, I've found it to be the lights and fringe atmosphere settings that cause the problem. My guess is that with each version of the app, Vue's light engine gets tweaked and therefore something that looks spectacular in an older version doesn't always look as good in later releases.

Just my .02, but what I've started doing is building my scenes and setting up .vob objects in Vue 6 and then lighting them in the latest release which seems to eliminate any surprises.