Okay, it happened again. After some time, I get a delay in pushing buttons on my joystick and it looks like if I move my stick in the pauses, the range of the axis gets changed and makes the stick unusable. It's even changed in windows, which I thought is impossible for this stick.
I have a MS PP1 USB which can also be plugged via gameport. After doing this, I had no problem anymore/so far.
This doesn't happen in AH1 and it didn't happen up to beta 28, if I remember correctly.