I haven't played in a long time, but I tried it again this weekend with the alpha16_4 version on windows 7 64bit.
Everything was doing great the first few games (other than me losing) but in the middle of my current game, my FPS suddenly went to 20-29/0.
I tried the CPU affinity changes suggested in other threads but didn't notice any difference.
At the time of the slowdown, I had just conquered the dwarves, summoned 20 imps, and sent my imps to claim tiles and collect items.
Starting a new game seemed to work fine. Eventually I tried reinstalling everything and at first it was slow but eventually sped up. But then it just happened again.
It happened right after I sent imps to build eyeballs near the human town. Now the FPS is slowly crawling back up from 20/0 to 20/17 at the moment. It seems like the cause might have something to do with pathfinding over great distances with lots of open space. I can certainly speculate why that might be a major cpu killer.