I can also confirm that calibrating the stick fixed this 'issue' for me.
I had also been getting very frustrated with the autopilot 'not working', I was convinced that it was either my X65 being faulty or a something being changed during an update (which, after reading this thread I realised had happened).
So I took the advice on here and calibrated my Logitech X56 using the Logitech software and sure enough that has fixed the problem.
I do not have any deadzone on my stick either.
The autopilot now works like it used before the update.
I thought I would share my expereince since I was also convinced something was not working correctly.