Timing is marginal, even at 57600 baud, and the APM typically has a ceramic resonator rather than a crystal (less accurate).
Some people have had better luck running at 76800 baud, which the ATMega can more accurately approximate with an 8 MHz clock.
See: http://yveaux.blogspot.com/2014/07/changing-arduino-bootloader-to-optiboot.html for instructions.
Note that if you need to recompile Optiboot, you may need to use a 1.0.x Arduino IDE (not 1.6) because some of the tools used for optiboot compilation (eg: make) are not longer included in the 1.6 distribution.