For now I've just noticed this issue in Capella, so we'll use that as the test case to see if this problem is any more widespread.
I recently set up a cool event in FRED that would create a Capella background using add-background-bitmap SEXPs. After setting up all 25 add-background-bitmaps, based precisely on the nebula backdrop in the MVPs version of 'Apocalypse', the final FS2 mission, I booted up my test mission to admire my work.
To my shock, it seemed like the event had bugged out. There were only two patches of nebulae in the sky, unimpressive and fairly distant. It was mostly just blank starfield. Weirdly enough, these two patches consisted of a total of 25 bitmaps, layered on top of each other.
Then I realized the problem wasn't my SEXP - it was the MVPs!
At some point the nebula backdrop on Apocalypse was cut down enormously from retail. For comparison, here's a retail screenshot in FRED2.

Notice the fairly diffuse nebulae backdrops. These continue for about half of the sky - you can see more of them to the right of the planet:

By comparison, the same two space areas in the MVPs. The first shows one of only two nebula areas in the background - notice how much less area it covers.

The other side of the planet - nothing there at all. Same true with above and below.

The last weird thing is the star itself. Retail doesn't have any nebulae near it, perhaps to focus attention on the Saths.

But the only other patch of nebula in the MVPs aside from the tiny one to the left of the planet is a big orange splotch to the right of the star:

Perhaps this was introduced in some kind of strange jab at REALISM. D: I would like to express my strong preference for the more cinematic, diffuse nebulae in retail.
Axem and I checked out other system backgrounds and Capella seems to be the only one with this issue.
ed: If I have made any huge factual errors in creating this, please make fun of me forever. It is a distinct possibility.