Sounds like a LOD problem to me.
I'd suggest you wipe out the caches* first to get rid of any possibly corrupted IBX files. Then check that you have the FS2's own graphics settings maxed out. You could also try re-downloading the mv_models.vp file. Other than that, I can't help, but those that can will need to know some things, like:
-what build (executable) are you using?
-does this behaviour extend to retail also? Meaning, if you disable the MediaVP mod folder, do the ships still pop up at certain LOD distance?
*Caches are directories in game/mod folders where temporary data is stored to speed up loading times. Sometimes the files get corrupt. The relevant caches here would be
../Freespace2/data/cache/
and
/Freespace2/mediavps/data/cache/
Get rid of those (the game will automatically re-generate them, so no worries
) and try again.