Hi Peter,
I'm an user, not support, but I thought I will share. I initially had problem with autopilot in several planes (e.g. Cirrus SF50) but this has changed with recent updates.
I have never had problems with 737 (all knobs work well) or 747 (v/s works in -400 and -100), but I noticed that sometimes I need to move slightly right or left in the cockpit to use knobs.
What is more autopilot will make mistakes if simulation is not fast enough (e.g. if I speed up simulation autopilot will have troubles keeping plane leveled). Is it possible that your simulation is running with lower than mentioned in manual ~20FPS?