Thought I'd throw these into the fray, and see if anyone else is having similar issues.

I'm pretty loyal to the Vasari at this point.  The cap ship that can drop siege platforms (for dealing extra damage to planets) tends to drop them out of range for them to fire at the planet.  This is when I leave the ships to their own devices - if I order the ship nearer the planet than it would go by itself, when it then drops the seige platforms, they operate just as they should.

Also, during larger battles, I'll notice that much of the weapons fire "disappears".  I can still hear it, and the damage is still being dealt, but pretty much all the non-missile-like weapons simply aren't visible.  A way I've been "solving" this is to save my game and re-load it.  It could be a hardware-related (compatibility?) issue - I'm running two GeForce 8600GTS's in SLI.