Ah, right... hmm, I remember something similar to this issue... where weapons fire was surrounded by black boxes. I forget the fix, but can you post your argument list from your "Feature" tab in the Launcher here? eg, mine is: (yes I know its a BtRL exe, that's fine)
C:\Games\FreeSpace2\fs2_open_3_6_9_BtRL.exe -spec -glow -env -jpgtga -mipmap -nomotiondebris -2d_poof -missile_lighting -dualscanlines -targetinfo -orbradar -rearm_timer -ballistic_gauge -ship_choice_3d -3dwarp -warp_flash -snd_preload -ambient_factor 0 -no_emissive_light -fov 0.55 -spec_exp 16.7 -spec_point 0.6 -spec_static 0.9 -spec_tube 1 -cap_object_update 0