I think the point here is that Scott is not saying they are running in the wrong direction, but that the setup changes from one power up to the next, which sounds to me like Mach3 is not saving the configuration correctly or its being overwritten OR very remote possibility there is some earth loop or other interference which is cause the drives to misbehave..

Scott - when you go back into the ports tab are the settings changed or are they missing completely... i.e. the default MACH3 state? Have you defined a machine specific profile and select that each time when you start MACH3 (or is MACH3 starting with a defaul profile - does it have /p in the shortcut you start it from?) - see page 2-7 of the MACH3 manual. (sorry if you've been round that loop, but we all need to get to the same starting point)