Calibrated ESC changes in ardupilot

Ardupilot apm2.8 setup everything in missionplanner except esc since won’t update to 3.3. Therefore I calibrated each ESC separately with the receiver. Each one worked as it should.

Attached to ardupilot, armed and started. Motors did not start at the same throttle.
motor 3 started much later than motor 1, I switched 1 and 3 in ardupilot and tried again
now motor 1 starts later. In other words, it is not the ESCs, it depends on which motor is plugged into motor three pins on ardupilot. Something in not right with ardupilot. Same motors and ESCs with a different controller work fine but not with ardupilot.

What could be wrong in ardupilot to cause this behavior?

Anyone have an answer?