OK, fixed it!
Thought I'd post the answer here should anyone else have problems:
Basically the acceleration on my soundcard was too high! A mate and I think that the more "advanced" features on the beams, like echos and what not, were getting jammed somewhere along the way. Reason being is my framerate has also been improved. I know my graphics card is poo, but it should still breeze through FS2.
Anyway, I toned down the accelration on my sound card and it's fixed ALL my problems (Except the afterburner, but 95 and/or 98 compatibility fixes that)
So there we have it. Framrate issues affected by sound. Odd eh?