This isn't technically a bug, so I didn't post it in Mantis. It's more of a performance issue.
I'm using FSO 3.6.9 RC 7 and the Zeta media .vps. The FPS usually stays at about 75. However, anytime a capital ship uses a beam larger than AAAf, the game drops to about 5 FPS. It doesn't matter if I'm facing the ship that's shooting. To complicate matters further, it will sometimes occur in the beginning of the mission for the first few shots, then the problem vanishes. It also seems more common when I'm about 5-8km away from the firing ship. If I'm close in it doesn't occur or isn't as bad.
My system specs:
CPU: Intel Pentium 4 3.2GHz w/ HT
Mobo: Intel Rock Lake D865PERL
RAM: OCZ 2GB Dual Channel DDR, 2.5-3-2-5
GPU: 256 MB ATI Radeon 9800XT AGP 8x
HDD: Western Digital Caviar 120GB, SATA
OS: Windows XP, SP2
Flags I run FSO with:
-spec
-glow
-env
-jpgtga
-mipmap
-nomotiondebris
-missile_lighting
-cache_bitmaps
-rearm_timer
-ballistic_gauge
-ship_choice_3d
-3dwarp
-warp_flash
-snd_preload
-fps
-allslev (Don't ask. I know it's not supported in RC7 and that it doesn't do anything, but FSO won't run without it.

)
I've also tried removing all the graphics flags except the jpg/tga textures, missile lighting, and disable motion debris ones.
I think that's everything, but I feel like I forget something...
Any help would be greatly appreciated.