I Found a solution to the problem; I changed ESCs to Tiger Motor ESCs and changed the signal to 200hz.
More tunning on PID required, will try Autotune, however quad flies great on stabilized mode.
It is now clear that the problem is not related to PIXHAWK but to the ESCs and signal processing by the motors . As previously mentioned by experts in this Forum, the signal for Pixhawk is always the same and the controller is not the problem.
Ok I accidentally sent a message to all the group, but I meant to make a clear declaration about PIxhawk.
For some reason, no one has ever found a resolution with the motor sync issue with some ESCs,( in my case with hobbywing 40a and 60a and the sudden loss of control of the Pixhawk due to signal malfunction with low RPM high pole count motors ( t motor 4008 380kv).
I believe it is important to mention, that after tunning, changing ESCs checking motors, and a few minutes of Stabilize and Loiter flight mode flight, switching to Pixhawk has been truly disappointing, and everyone should no that it will take some time to reach the " industrial" reliability and end user friendliness of the DJI Wookong M in the Pixhawk.
I believe it will be possible, but when there are potential to date unsolved issues, the community needs to be aware of them, in order to create proper expectations of Drone Builders and developers.
Pixhawk is completely incompatible with hobbywing Pentium 60 a and Hobbywing 40a ESCs. It Flips on necessary roll adjustments, and the motors are completely out of synchronization, even after adjusting RC signal parameters, PID adjustments, ensuring good connections, and checking motors and ESCs.
I truly hope the solution will be using DJI or T motor ESCs; however, there is a lot of people that are likely to try Hobbywing, or other brand high Amp ESCs with large motors, and my message is:
DON'T try it!!
You will spend more money, parts and time and brain power than simply using another controller.