For quite a while now my FSO install has been going downhill and this is yet another problem. I'm not too sure how to explain this one, but following what was said in this thread (
http://www.hard-light.net/forums/index.php/topic,44733.0.html), I did a (incomplete - not enough HDD) defrag of the hard drive where my FS2 was, and my problem's been partially cured. Whatever I say next will be the current state of my problem after defragging.
When playing the MediaVPs as a directly loaded mod, everything shows up fine. But when I'm playing, say Transcend, (1) stuff like the cockpit glass reflections (Shine maps or whatever you guys call them) don't show up in the F3 viewer. (The cockpit glass is there, but it doesn't reflect.) And viewing the HTL Zeus which I added, or the HTL SD Lucifer, (2) I see the HTLed model in the F3 viewer, but with really ugly textures, like those that came off an LOD1 or LOD2.
Loading up a mission flying the Herc II, (3) I get a retail Herc II instead of the HTL one seen in the F3 viewer in the
same mod. Similar problems happen with other ships - (4) I see lower-detailed LOD's/textures on capships and fighters even when I'm only 200-300m away. Very noticeable when I look at things like a Deimos or a Horus where I don't see the LOD0 even when I'm close to point-blank range. And I don't even think the Deimos that I'm looking at is an HTL example - the textures on it are so blurry and it looks more like a retail one.
There is also a possibility that the MediaVPs-specific background nebulas don't show up in some of the missions. And as an oddity, the MediaVPs weapon effects are working fine.
Any ideas?
I'll drop pictures if words aren't enough in describing my problem. 
Not reporting this to Mantis because I think it's something on my end, maybe I still lack the HDD space, but I'm still stumped even after defragging and deleting a game (which got me roughly 1GB more, and I even defragged again after removing that game).