Yeah, looking through the MV_Effects.vp reveals some irrelevant files that have slipped through the net (unused shivan beamglow [S_BeamGlow.dds] and terran beam textures beam-green*) as well as a bunch of ani files that still aren't converted to EFF/DDS format... Oh well, work to do for the future MediaVP's.
What comes to those strange faint boxes, I'm not sure what's up with them. Certainly they aren't ideally made effects, but I can't help but wonder if they are still intentionally as they are, even despite the, eh, strange design. In-game they are only visible if you stop the game and look real close at the weapon effects; otherwise they create a faint glow.
I'm leaving this for someone who has done something with the weapon effects before and perhaps even knows what's going on with them.
The Shivan beam looks like some texture gets consistently corrupted during caching for some reason I can't really fathom. The files are intact on the VP, since hashes match, but something goes wrong during the process from HD to display, but what exactly causes it is a difficult question...