This is definitely a bit excessive. It shouldn't take more than a minute. If you are sure it is not a corrupted save there must be something wrong with your system. Lots of things could be wrong, we need a lot more information to help you. Check out what other processes are running on your computer (right-click the bottom bar in windows and select "job manager"). Repair your directory (CCleaner is a nice free program that does just that). Go to the windows/vista club and read what those guys there have to say, they helped to squeeze quite a few more fps out of my rig. If you tried all the tricks in their book (disabling Aero, remove stuff from your desktop etc.) and it still takes forever, reinstall windows.
But before you do that, check if your DF setup is okay: Download a new copy of DF, try your save on another computer, stuff like that. And if you are using Steam, check that it is not updating some big game in the background. Last week I had a sudden decrease in overall performance, and I went through all the tricks, but to no avail. Just before I decided to reinstall the whole lot, I checked Steam, and guess what: Steam had decided that now was the perfect time to download 20 gb updates without telling me. So now I have have a top-tuned system that can easily make 15 fps in my fort of 220 dorfs.
Reading your post again: I get more and more convinced that your save is corrupted.