Some area of the game are just very unoptimized also. While one system will run amazingly well with lots of detail the next will run like mud because some of the effects are not optmized or the scene needs a few optimization passes to get rid of the offending feature. I mean if you test these zones on the lowest settings you can easily see which is working well and which aren't. Given some time and some pressure they will probably look to improve the performance. Do a /bug if you find a system that runs horribly slow. Larger scale raid zones will require less detail settings to run well on most low to mid range machines.
Are all your drivers up to date? I ask because it seems its a problem on your system, be it a bottleneck, memory leak or driver conflict.
Reason being, not many people are reporting this at all.
I'm having this problem as well, it seems to occur randomly, i had no issues during the starbase 24 fleet battle with tons of ships but this has happened fighting one NPC in a system with noone else present.
my computrer is a core 2 duo 2.4ghz 6 gigs of ddr2800 and a ati raedon 4850 1gig card.... the game riuns great, this just happens randomly and it's really frustrating during a battle.