So, if I'm understanding this correctly, the only thing the M3 is doing is setting one of the PP outputs to command the motor on, but that signal is basically going nowhere, right? That sounds like a flaky BOB.... I did have that kind of problem with my (really old) Rev 2.0 C11 board, but since getting a Rev 7, no problems at all. I wonder what the differences are between my Rev 7.0 and your rev 5.4?
Regards,
Ray L.