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I have downloaded the game several times, with and without the downloader and the setup will not run it just does nothing. I have tried on two computers one XP and one Vista both with the same results.

I managed to get an original copy of Freespace from a bargain shop, for less than gog charged me I may add, and it works perfectly.

Wish I'd got it before paying gog for some rubbish that doesn't work, I see from other posts that I'm not the only one having trouble with the installers so be warned ;)

Ah well rant over, on to new things!
This is odd. It's been cropping up with some games and I'm not sure why. The game does work and install - I've done it myself several times. Did you contact GOG support about this? If not, you should.
I installed yesterday with no issues.

Try installing it with Administrator profile.