Auto mission problems

Hi there, collegues.
I’m using Pixhawk with copter 3.3.1 firmware and having problems with Automatic mission.
Our Quad have to land twice in a single mission, but on the way back its speed decreased from 4 m/s to 0,6 m/s.
Mission look like move forward and return just the same route (we are not using RTL, yet).
Our small hexa drone running APM 2.6 with 3.2.1 firmware passes typical mission just perfect!

What causes troubles on back flight( back to launch point after land) using Pixhawk??

Thank You.

P.s. All sensors are calibrated, we have 12-15 sats, EKF is in order anytime.