I too have the TM T.Flight HOTAS X and had some issues with setup at the beginning - which turned out to be my own fault. Here's how I solved it:
First, are you all sure you have your joysticks set to PC mode and not PS3 mode? I made this mistake when I plugged mine in for the first time and the joystick didn't operate properly (the ONE time I didn't glance at the manual first - live and learn).
To "fix" the fact that my PC now saw my joystick incorrectly on my OS (Win7 x86) I had to unplug the joystick, remove it's remnants from Device Manager, reset the switch to the "PC" position and then plug it back into the USB port. Windows redetected it and I tested all of the axis controls in the Game Controller applet in Control Panel, just to sure. I also set the joystick for 5-axis mode (home button green).
Once I did this, Freespace would "see" the Z-axis of the throttle when I would attempt to bind to it. You can use the absolute or relative throttle control - both seemed to work exactly the same in-game.
Also, since there are no real "slider" commands in Freespace to bind to, the nice rocker/slider switch behind the throttle handle will go to waste unless you use it to rotate the ship left/right (RZ axis). I prefer to do that by twisting the joystick instead.
So what I did to use the rocker/slider switch as 2 more buttons was to use the reprogramming commands in the joystick (consult the manual) to have the 2 useless buttons on the base of the throttle (top-front of base) switch places with the rocker switch on the back of the throttle handle. This way, in Freespace, I could bind the right rocker "button" to the afterburner and the left rocker "button" to the energy equalize setting. To me it seemed more logical to have all of the ship attitude controls (including ship rotation) on the joystick and the speed controls (including afterburner) controlled by the throttle - of course YMMV.
Hope this helps.