As far as Mach4 and the PMDX-411 are concerned, you shouldn't need to reset/restart them periodically. A wild guess here but could it be possible that the microstep settings on your driver didn't "take" until power was cycled on it??? The manual for the DM542 doesn't explicitly say whether the DIP switch setting take effect immediately or require a power cycle to take effect.
If you have "rollover" enabled, Mach4 will limit the motor's rotation to a single 360 degree range. If you move to 30 degrees, then move to 300, it will NOT continue if the positive direction. It will instead go backwards through 0 degrees, then to 359, 358, etc. until it gets to 300. I believe for your application you need to disable "rollover".
Bob