@iceman24: Thing about the yaw-no turn/turn-no yaw thing is: I don't think you can actually have both assigned at the same time(?) 
No. If your joystick has enough axes available, you can definitely have all main control axes bound to separate axis movements at the same time. And you definitely SHOULD. Pitch, roll, and yaw are all important.
If you're used to normal flight sims it might be best to just have yaw on so you can fly like a normal plane. If you're used to space sims then maybe have the turn activated.
Normal fixed-wing aircraft use primarily roll (ailerons) and pitch (elevator) to maneuver. The yaw (rudder) is used to coordinate turns so that the aircraft flies through the air with as little slip angle as possible, or conversely to increase the slip angle to slow down the aircraft by increasing the drag. Rudder is also important in recovering from abnormal flight envelopes such as spins.
In this light it seems odd that you would suggest someone used to flight simulators to use yaw instead of roll. However, there's a pretty big difference in intuitive flight controls when you're in an aircraft, versus floating in space where your attitude doesn't really affect things like direction of airflow, amount of lift or such stuff that is vital for aircraft.
Interestingly, I have had some control issues where my intuitive control wirings in my brain switch between aircraft/FreeSpace style of control, and I haven't been able to figure out whether I prefer having roll axis on Joystick X axis, and yaw axis on Twist Handle, or vice versa. It seems that when I'm fighting, I sort of prefer the latter (FreeSpace style bindings) while when I'm landing on the Theseus, my brain switch into aircraft mode. I think it's because the visual reference has some analogies to landing on a carrier, which I've always done in an atmospheric aircraft.
@iceman24: My personal experience with Logitech sticks is that they are atrocious pieces of hardware and the software is not much better. I would not be greatly surprised if Logitech had decided to derp around with either the driver software or even the hardware itself, making some sticks different from others, or work a bit differently, which could cause some sticks to work differently with FSO.
However, it feels more as though there is something simple that is either being overlooked or done wrong.
Do you have any additional game controllers (virtual or real) on the computer?
Can you describe the process with which you try to bind the axes to the controls, and perhaps show a screenshot of your controls configuration menu in the game? There is a history of the binding method being somewhat unintuitive since many people in the past have had problems getting it working.
Also, the debug log will definitely show what the game is looking at for control inputs. I think it's clear your game is reading the joystick somehow, since you get some inputs, but the debug log will show it for sure.
If nothing else works, there's still something you might try: Completely removing the Logitech joystick driver, and using Windows' own default HID driver.
I've found that sometimes Windows' own driver seems to work better for sticks like this than any drivers that the manufacturer likes to throw at you. For example, you get the ability to manually calibrate the joystick and to actually confirm that it IS calibrated.
The downside is of course that the profiler won't work, but I don't think that's a critical feature for Extreme 3D Pro (it's a really simple stick). However you can always re-install the joystick drivers and/or profiler software.
Good luck.
