If the green light is flashing then its good to go and you dont need to worry about the alarm and enable for now.

One clear difference running from mach and pro tune, is pro tune is going direct into the drive where as mach is going via the bob. From your description, your feeding +5 to step and dir pins on the drive and im guessing the step and dir - pins go into your bob? Are you sure the bob is wired right? ie is the dir - ment to be wired into the bob, meaning its syncing and not sourcing?

Regards

Trev