Biggs427,
Do yourself a huge favor. Switch the limits to 24V logic. How? You basically add a 24V relay. How? The 24V power is run through the NC and COM contacts of each limit switch, then to the relay. Now in the un-faulted situation meaning none of the limit switches are tripped the 24V is active, meaning it is turned on. Now the contract of the relay will connect to your breakout board. The common will go to either Ground or VCC (5V) depending on the logic you want in your breakout board. The NC contact will go to the LIMIT switch input on your breakout card. The relay should be kept close to the breakout card. Why does this work? The noise impacting your system is raising the low level just slightly so the BOB thinks it is momentarily seeing a high. When you have 24V logic or even 12V logic the logical one is so much higher the noise will not ever be seen as an activation.. This is how commercial machines are wired, and they is why their controls always use 24VDC. Keep in mind if you don't have 24V handy you can also use 12V, just change the relay to 12V, both are well above the 3.3-3.5v that can be interpreted as a high.
Russ