My Pixhawk is installed on Mariner quad (500). With the version 3.2 it has many nice flights, with very good ALT Hold control and AUTO flights.
After recent upgrade to 3.3.2, it changed its behavior: in Stabilize all is OK, stable and smooth control, hovers on 50% Throttle. When switch to Alt Hold, it starts rising up at full throttle! When switch back to Stabilize, all is OK with the control. Sometimes the rise up is hard to compensate with the trottle…
Looking at the logs, all seems OK, except the inconsistency in the IMU - accelerometers 1 and 2 shows different phase after switching to Alt Hold.
Do you have any explanation? Hardware fault or 3.3.2 software bug?
With 99% accuracy, its a vibration issue. You need to dampen the Pixhawk better. Even small vibrations will cause this to happen. And its hard to find a good vibration dampening material.
But here is a thing that will help you alot:
Open your pix, and add weight to the bottom plasic case (about 15-20g). Secure it in the middle of the case.
Use a dampening silicon material in the top case, so the board can´t move at all. It should be thick enough to put pressure on the board when you close the case.
Use 3M 2mm double sided tape to mount the Pixhawk, as close to origo/CoG as possible.
This will very likely help with your issues.
We now use this method on all our large UAV´s using Pixhawk. We had the exact same issues as you before. Reason is the poorly designed Pixhawk, with IMU mounted without dampening.
The main problem is the buzzer - in small watertight closed body, the sound jamming the IMUs. In the 3.3.2 every mode change event is sounded!
The other software issue was because the 3.3.2. using IMU2, that gives different reaction to the buzzer sound, letting the controller to raise up. The previous software used IMU1.