This is weird. I second what The Joshi says. The mouse is excruciatingly slow on the menu (ie. the high-res bit where you get to choose between playing the game, setting up the sound, and so on), but fine once you get into the game itself.
FWIW, I have a Logitech PS/2 mouse and I'm playing the budget re-release of FT. As for the DOS mouse driver, it's a generic-o Logitech one that came with Windows 95.
There is hope!
UPDATE: OK then. I just tried it on my new(er) computer and the problem occurred as described. This sucks!
I'll look into it a bit more if I can be bothered (don't hold your breath