First, you're having a memory problem in some form or fashion. Please remove the -pcx32 switch from your command line and see if that helps at all. That switch is somewhat depreciated; it's not obsolete but it causes so many problems that it's no longer a launcher option in newer builds.
Secondly, the version of the 3d shockwave that made it in to mv_adveffects.vp is way too high-end for most normal systems (yes, including yours, as I have one strikingly similar that suffers from the same problem). It takes forever to page in, relatively speaking, and IIRC it doesn't really get loaded until it's used in mission. As I don't think there's another source for a shockwave in "Surrender, Bellesarius!", the game won't stall until it tries to load that in. If you can find it with search broken, I suggest downloading a medium quality version of that effect and placing the image and eff files within it in data/maps.
As for 2, I believe afterburner trails have been removed from media VP tables for some time. You shouldn't be seeing them at all. Unless of course you mean you don't see the thruster graphics change when a ship engages afterburners, which is strange and probably indicitive of a real problem. A lot of that has changed significantly in recent builds and thruster graphics still aren't fully up to snuff, so there's not even a good way to test if it's changed lately.
Lastly, you'll have to provide a screenshot of #3. I think I know what you're talking about, but I'd like to see it before I start barking up the wrong tree.
