I'm having some serious issues setting up my Saitek X-52 pro with this game. If I change the controls from the default in the options menu, the game crashes pretty much as soon as the loading screen opens. If I leave them as default, the game runs fine, and the joystick works too, albeit with all the controls in the wrong places.
Has anybody else had this issue with another stick, or is it specific to the x-52?
I'm also running windows 7 64 bit.
Many Thanks
Sam

Hmm, that didn't work unfortunately. However I did just notice that an error dialog pops up very briefly when it crashes. So fast in fact, that I can't read it.

You should try to contact with GOG about your problem.
http://www.gog.com/en/support/contact/technical_issues_with_games/aquanox
Unfortunately I don't know a solution for your problem. :(
It's so bad the default configuration?

Actual settings are stored in Application Data folder (or in this case some Win7 equivalent), so it's very likely that crash issue is connected with permissions, as Namur mentioned. Even running as admin sometimes doesn't help.
See if you can locate your settings file and change it manually. (In Win7 it would be in c:\users\%username%\appdata\roaming\Aquanox ...I guess.)
I don't think it's a game issue, it can handle custom controls quite well (at least with latest Saitek drivers and Cyborg Evo).