@Daniel-Mellinger
I am still facing the issue with the remote, but i believe its only with the remote as I was able to get it flying in offboard mode using the VIO onboard. Its flying and is quite stable at the moment. Due to the nature of our research, we dont fly with the manual remote (we only use that for initial tests).
But from my experience im not sure if the remote controller could be at fault, because
I have used the same RC / receiver pair on the VOXL (version 1) and its able to fly in manual mode without any problems
If you look at the Manual Control input plot in the px4 review mentioned in the 1st post, you will see that there are no discontinuities present in the signal. The setpoint thrust and pitch curves look fine. Whereas the setpoint pitch and thrust going into the attitude controller is quite discontinuous
In summary, we are just using the remote to change modes and trigger emergency kill switch and thus this bug is not affecting us anymore