I'm no expert, but I've found that for some games I need to set affinity to only 1 CPU. If you've never done it: after starting game, bring up task manager (cntrl/alt/del), go to PROCESSES tab, find your game name, right click, then click on Set Affinity. Uncheck either cpu1 or 0 (doesn't matter which). Go back to game...hopefully it will run fine.
Another thought...are you running Impulse first and GalCiv from Impulse? If so, try not starting Impulse and just using the GalCiv.exe to run it (or a desktop shortcut)
Good Luck with your game!