First confirm the RC channels are all mapped correctly. Do you see the correct behaviour of throttle/yaw (left stick if mode 2) and roll/pitch (right stick if mode 2) coming through to Mission Planner’s RC calibration screen? Do you have values ~<=1000 and ~>=2000 detected/calibrated by your movements? e.g. with a Taranis the lower is ~988 and upper ~2012.
Once that is confirmed, then we don’t need to talk anymore about RC input and can focus on the output/ESC/propellers. Did you double-check all motors are spinning the correct directions, and props are the correct way around. Usually that means the writing is on top and you bought different (CW clockwise and CCW counter-clockwise) propellers, installing them on the appropriate motors. On the quad X they should be spinning so that the propellers are pushing against air from the side around into the middle front/back ends of the frame.
Check your ESCs are programmed and no advanced options are enabled. Even if your ESCs don’t support flashing there should be a “programming sequence” or card which enables or disables various settings. All ESCs must have the same firmware and configuration.
Check for dry solder joints if you did custom work on the cables to tidy the build. Use a servo tester on each arm/ESC input to confirm the behaviour is as expected (somewhere near lower PWM start to somewhere near upper PWM full power) and that no excessive heat is generated by the ESC during light/testing operation (bad ESCs and motors are common enough when buying relatively cheap mass produced products).
Check there is absolutely not more than one power input connected to the Navio servo rail. The only device connected to power (output) should be the RC receiver unless you have servos for landing gear/gimbal, etc… Disconnect any other devices from the servo rail until the motor problem is fixed.
Reset all APM settings to default with the current Mission Planner software and don’t use the wizard to configure it. Manually click through the Mandatory Hardware and the Battery Monitor and Motor Test of Optional Hardware. The Motor Test is probably the best point to stop at when it doesn’t work. Then describe the exact behaviour and share the logs at this point (best on DIY Drones forum but we could also try to understand it here) for further diagnosis.
You could also try the master build, then the new simplified ESC calibration should work. But that shouldn’t be necessary because the Emlid apm.deb build is stable for many other people. In case you want to experiment with 3.3.2 “master” this procedure and script will load that easily for you: APM 3.3-rc9 beta testing - #23 by CodeChief