So, over the weekend I reflashed the Repetier firmware, and I was able to get the printer to stop when the Z_MIN endstop was triggered, so I know it is not a hardware issue, it is a setting in the Marlin firmware. Due to the lack of replies to my request, it doesn't look like anyone else knows how to fix this problem either. Guess I'll keep working with the Repetier firmware and see if I can get it working better. I like Marlin better and was hoping to use it, but can't seem to get any resolution to this.
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