I just played through "Surrender, Bellisarius" and noticed only a few problems:
First, is the nice square-shaped damage decal supposed to be there when the Psamtik's beam punches through Bellisarius's hull?
Second, only real slowdown is with effects, not ships. Both transports and all three of my wingmen against a nebula background doesn't even dent my framerates. Kudos on tightening the code so much.
Third, and this one is almost certainly media- rather than build-related, the really, really pretty explosion has a really big drop in frame rate associated with it when the Bellisarius goes up.