Thanks Mark4!
I looked into switching to 24v signals at your suggestion and it looks like that's probably a good idea. Those MB3 boards do look like an improvement from what I am using, but I think first I'll try using a 24v to 5v optocoupler on the problematic inputs and see if that helps. (the price really adds up for those MB3s for a lot of machines) If anyone has any opinions about that I'm all ears.
I don't know what a contractor box is, but I think I get the idea. I'm sure I could improve on the wiring going into the machines. It is all very neat and professional looking from a physical standpoint, but from a noise avoidance standpoint maybe not so much.