This little program emulates a joystick that uses your joystick for input. If alleg doesn't recognize your joystick, this is the workaround. As an added bonus, you can alter your joystick sensitivity and deadzone.
First, download vjoy and install. vjoy is the virtual joystick driver.
VJOY
I chose to install the configuration application only. Once installed, you don't need to configure it unless you have multiple joysticks and wish to configure each to be available for UJR to use. If you want to launch and configure vjoy, you'll find it in the list of installed programs on your computer.
Second, download Universal Joystick Remapper
UJR
Notice in the upper left of the photo (below), that the vJoy Stick ID is "1" and that it is "Connected" as shown in green print. Also note, that the Physical Stick ID is "1" for the X and Y axis that I elected to use. I selected to use only the X and Y axis since they are the only ones I needed to alter. My rudder and throttle slider work adequately so I elected not to have UJR "see" those. I could have taken the time to map every axis and what not, and still I could have elected NOT to map to those to UJR within Allegiance. In other words, just because UJR now maps to your stick doesn't mean that your game will be using UJR on that function unless you tell your game which "stick" to use. As you can see in the photo, the X and Y axis show values on the right hand side. You'll know you have it working correctly when you see those values on the right correspond with your joystick movements.
Unlike vjoy, UJR is not "installed" on your computer. You will have to goto the folder that UJR resides in and launch it from there every time you want UJR to be active (while playing).
While UJR is running in the background (minimized), launch allegiance and hit ESC G C and scroll to the bottom and highlight the axis you want UJR to manage. If you only have one physical joystick installed, Allegiance will have already named it "Joy 0" within the game. While that axis is highlighted in Allegiance, hit the Enter key and move the joystick until the "Joy 0" (your physical stick) changes to "Joy 1" (UJR). You may have to do this multiple times until Allegiance sees the "Joy 1" instead of "Joy 0". Do this for any other axis you want UJR to manage. In Allegiance, my X and Y axis show "Joy 1" and my rudder and throttle and hat are mapped to "Joy 0". Once you've got it configured, click "Accept" and give it a whirl.
As I mentioned earlier, the best part is that you can alter your deadzone and sensitivity with UJR.
Just for thought:
Vjoy by default, emulates every button, axis, slider, hat...that is on your physical joystick. Esentually, vJoy is a duplicate joystick of your physical stick. This is why you don't need to configure it because it already makes anything you have, to become available to Universal Joystick Remapper.
UJR's job is to take what vjoy makes available and allow you to turn it into whatever you want. You could map the X axis to the Y within UJR (which would funk out Allegiance) however, you could then configure Allegiance to use the X instead of the Y and thus would be correcting the funk that UJR was imposing.
The point is that by using these two programs, you can make just about any controller do anything. You could have multiple controllers mapped to different functions within Allegiance. I'm not certain, but I think this can also map physical rudder pedals to the rudder (or any other) control in Alleg.