My joystick system worked fine with beta 44.
With the final release, the software now doesn't recognise any joystick buttons. AcesII recognizes x,y,and z axes on my joystick, but no z-axis on my CH throttle. My rudder pedals work, but no joystick buttons makes for firing weapons a bit difficult.
I have a CH-combat stick, CH throttle, and CH rudder pedals attached to the gameport of a Creative soundblaster sound card, with the latest CH driver workaround for Windows XP. The $50 sound card option was a lot better than buying all new USB controls. My setup worked fine in all the betas. The CH combat stick buttons 1-5 buttons and 4 position hat switch worked fine.