Ryan,
Not being familiar with your breakout board, I just went to the cnc4pc website and discovered they have different models. Which do you have? I looked at a couple of models that they offer and I'll say it again- Based on the diagrams CNC4pc shows at their site, IMHO you should not be sending ANY voltage to the limit/home switch circuit.
Me thinks that in doing so, something may be tweaked. Maybe not, did you do the wire test I previously described? And yes, BTW- 3.5-5v Will make a diff, so maybe you wanna put a meter on that too.
Sid