Patrick,
It sounds like you have checked thru the physical / mechanical issues. I would start manual tuning. I understand 3.4 has changed the terminology for “Stabilize rate P” regardless, it sounds like this is to low. I suggest after reading the wiki sections on tuning the PID settings, you manually change the stabilize rate p. First, increase the rate P by say, 20%, then arm and slowly increase throttle, don’t let it take off, just see if the flipping movement gets better or worse. If it improved then adjust rate P even higher, If it got worse, adjust lower. In the beginning you will need to provide some correction at take off. The objective is to get in the air and confirm Alt hold will work. At this point you don’t expect to fly very stable, just fly. The objective is to fly in Alt Hold so you can perform Auto Tune.
Patrick, I’m a relative newby, but I had a similar when I first set up my quad (not a hex). It was due to reversed orientation of the Pixhawk, which I assumed the accelerometer calibration would auto-detect.
Is yours mounted correctly, and is the orientation of it set correctly in the parameters?
I’m sure you’ve checked this already but couldn’t see it covered above.
Thanks to everyone for their replies and their time. I am a newbie and made exactly that mistake!! I carefully numbered the motors, the direction of rotation and the esc plugs associated with each and then mistakenly installed the Pixhawk facing backwards!! To compensate I had reversed the radio-controls but obviously the flight controller was acting in the opposite sense. Hours of head scratching wasted trying to figure it out ensued. I am pleased to report that after re-setting to the correct configuration resulted in a beautifully behaved and very stable Hexacopter. Such are lessons learned- often the hard way!
Glad to hear this sorted your problem. Sometimes I find it’s easy to get bogged down in details without seeing the big picture or the obvious problem. All the best!