Sounds to me like that's exactly the issue, and believe it or not it's not something the MVPs did.

The way beam sounds work is they play through in order:
| (warmup sound)(beam looping sound for fire time of the beam)(warmdown sound)
| (shot sound)
------------------------------------------------------------------------------> Time axis
Where the crappy above diagram is meant to show that the shot sound is played at the same time the looping sound starts.
Since retail, there have been two 'shot' sound effects, and something like half the beams have used the second one. However, no matter what the tables said, the engine used the first of the two. It looks like this bug has now been fixed, so the engine uses whichever effect is used in the tables.
Anyway, I agree - the second shot sound is crap compared to the first and really detracts from the overall sound of the beams. I'll see about setting all beams to use the first shot in the patch.
