Thanks Mathijs for the reply.
Well the first thing I did was to go to the settings and check the stick calibration. But everything looked fine there. So I did that via the windows gamecontroller settings, no problems there aswell. I can definately rule out a hardware related issue.
I restarted the sim than and everything was working. What I did before was to do the flight from LOWW-EDDF, parked at the gate, ran through the GSX deboarding/boarding sequence and set up the aircraft for the next flight. So there was no reloading of the aircraft inbetween those two flights. I basically waited about 15 minutes or so (that's when I did the flightplanning with PFPX for the return flight) and then continued the flight. So it was perfectly working before..
I will try to do that same procedure again the next time, maybe I can analyse it a bit more..