Are you playing standard Freespace 2 or have you downloaded the modern open source engine Freespace Open? I believe the latter should solve your problem (not to mention make the game look gorgeous).

This poster used Freespace Open and the in-game mapping to get his stick programmed:

http://www.gog.com/en/forum/freespace_series/playing_freespace_2_on_an_x52_without_profiles

He did mention a profile but indicated it was unstable - however maybe it was simply unstable with Freespace Open and wouldn't be with vanilla FS2. But with Freespace Open you should be able to use your stick and not need a profile.

http://www.hard-light.net/wiki/index.php/Getting_started

http://www.gog.com/en/forum/freespace_series/quick_and_simple_freespace_2_scp_installation_guide/page1

This is the profile I made, you can give it a try. Just remove the jpg extension and put it where the saitek software saves the profiles, on my computer it's in Vista's public documents folder for some reason. You do have to map the throttle ingame, but it should be easy, just go to the absolute throttle control, hit bind, then move the throttle to pick up the axis. I can't remember whether it binds banking to the twist axis automatically, but you might want to do that too. Unless you prefer your controls more like an aircraft, in which case you'll want to map twist to yaw, and the x-axis to banking.

I've recently started playing FreeSpace 2 (with the open source engine/SCP improvements) with an X52 (non-pro version), and so far, I've found that Saitek's profile utility is quite useful, since it allows you to use the mode selector and the pinkie switch, or to use the slider and rotary dials to emulate key presses depending on their position. Good examples (for me) include:
- using the slider for the afterburner
- using the same button for switching secondary weapon bank and for switching secondary fire mode (single/double) with the pinkie switch as a modifier
- using the wheel for next/previous closest hostile.
So, I'd say that just using in-game mapping isn't really a great solution, since it doesn't allow all those possibilities... Which are quite useful, since the X52 doesn't actually have a lot of buttons - it mostly has a lot of coolie hats and dials. The exception seems to be for coolie hats, which seem easier to map from within the game, but maybe I didn't understand how they work in the Saitek software. The throttle axis (Z), as well as the Jostick axis (X, Y, rZ) have to be mapped from within the game even if you use a profile for the buttons/dials/switches, so that's an issue anyway. A few questions that come to mind:
- Do you have the latest drivers from Saitek's website installed? (I know, obvious question, but you never know...)
- When you calibrate the joystick in Windows, do all the axis and dials get recognized? If not, there's a problem which isn't due to the game.
- As crazy_dave said, are you using the open source engine? There are no reasons not to use it AFAIK, and I suppose that it should handle modern peripherals better.

Fair enough - I'm only going off of the other user's experience. :) It's very possible he did something else to make his system unstable that had nothing to do with Freespace 2/Open.

I'm using a different stick - the T-Flght Hotas X. DO you people have any tips for targeting. I am finding that really difficult so far.

So far, I've mostly found useful to have the "target next closest hostile" and "target in reticule" commands mapped to easily accessible buttons (in practice, on the X52, I mapped "target closest hostile" on the scroll wheel on the throttle, so I mapped both the "next" and "previous" versions - but I don't think it's really necessary to have both). Also, I usually check that "auto targeting" is on at the beginning of the mission.

It seems to me that the other targeting commands are used less often, so I can live with accessing them from the keyboard. One exception would be the "target next bomb/bomber" command, which is very useful in some escort missions, so I'm thinking about mapping it somewhere - but then, it depends on how many buttons you have available...

Also, in another thread, crazy_dave gave his usual choices for his joystick, which has 12 buttons like the T-Flight, so I'm sure you could try it out. Here's the link :
http://www.gog.com/en/forum/freespace_series/great_game_but_seems_to_require_4_hands_to_play