your log shows homing axis letter and axis numbers at the same time if you home A axis only as motor 1 what happens, the motor numbers are the mapping function across all plugins`s Mach4 does not give a ********* what axis letter is set to a axis number as this is just the mapping of motor`s.
your problem is A axis so just run that by it self once you have done that a put up the logging, we can see what is going on with that motor then go from there