Danijel, Yoiu should have really created a new topic for your issue rather than jumping on an unrelated existing topic, but I think I can possibly help you. Can I make the assumption that you have an original Pixhawk PX4 v1 - maybe hardware spec 2.4.5? If the answer is yes, then there is a power supply issue on that hardware spec which affects one of the IMUs. I see your exact issue on my oldest hexacopter - and I have a work-around. The solution is that after first flight, once your battery is disconnected and removed, short out the power connector on your quad, this will discharge the capacitor of the supply to that IMU - hold that short for say 30 seconds, then remove it, and connect up your fresh battery, and hopefully the Pixhawk should work as well as it did on the first flight. It works for me every time. My newer v2.4.6 spec Pixhawk does not have this issue.