After two hours of corrupted logs and debug I figure it out. I´ve tried everything - changed SD, computer, cable, usb port etc. and always when I download the log from Mission Planner through the USB cable it got corrupted. However if I detach the SD card and insert it direct to my computer, the log was OK.
Started to play with conf and the culprit was that MAVLINK_protocol for serial0 ( usb ) was set to 2. If so, log gets corrupt. It could be a mission planner bug or firmware bug.
Back to mavlink version 1 and everything went fine!
Could you guys please test it to see if it happens to you as well? If so, I will open an issue. Thanks.
Windows 10 - Mission Planner 126.96.36.199 build 1.1.6220.13108
Com driver port from 3d robotics version 188.8.131.52