Hello,
i can give the all-clear. I have downloaded the game again, and replaced the two files Turrican2AGA.lha and Turrican2AGA_ol.uae on my USB stick. Since then the game runs again with my THEC64 joystick.
I'm sorry that I'm just getting back to you now, but I love the game and had played it (for testing) right back to level 3-2. :-)
I will play Turrican II AGA more often now in the next days and report again if the issue occurs again.
Many, many heartfelt THANKS for the remake of this great version of Turrican II. I love it!