I have the same issue, I have it while it's loading because it's using 99% + processing power to load the sim into the page file, go figure, I also get it on huge/gigantic maps during turns or if I'm clicking around on the screen while it's trying to think, not sure but it might have something to do with
A. bad driver
B. The fact I'm running on a 2.4 ghz P4 instead of a CRAY or Dual core
C. bad code that doesn't share the CPU efficiently

take your pick
should be in the 1.2 change log if it was up to me, but they want to add some flashy ship parts instead