I had a similar problem with Estops in particular. Slightly leaky circuits, long wires in particular, can trigger a pin. All my estops and limits feed into relays, which short the PC pins via a short length of printer cable. The relays run off my 9v control circuit that also powers the hall effect home switches. i used to suffer all the time from false Estops, now life is easy with relayed signal inputs. Why, i liked it so much i bought the company*

[/victor kyam]
* more relays, anyway

Okay, BluePinnacle,
  Please explain further your relay switches on the limit and estops, because this sounds good but complicated 
 Can you give us a diagram and description of your relays?
  Thanks,
   Glenn

Thats how I have it set up.  My E-stop opens the circuit going to the coil of my relay.  Once I hit the e-stop my relay de-energizes breaking the circuit that goes to my pc board.  I also run my control voltage that energizes the relay controlling my router through the relay so that it gets turned off as well.  My problem is that the diagnostics screen does not indicate the pin  going active that my E-stop is on. So I feel it may be voltage leaking somewhere else I just don't know where.     

That's about the strength of it, my 9v supply feeds the coils of several relays. One has its coil in series with the limit switches, the other in series with the Estop mushroom. Hitting a limit or punching the mushroom cuts the current through the coil and allows the NC contact of the relay to snap shut and short out a pin. (10 for estop iirc).

The relays areTyco T7S S5E6-12 single pole changeovers, about sugar-cube sized, 57pp from RS, part number 616-8714. They're 12v rated but run fine on 9v.

Hey BluePinnacle,
  Thanks for further detailing your set-up, I am anxious to assemble a system like yours, and knowing what size relays to buy helps alot. I appreciate your help!
Radio Shack, here I come,
  Glenn

np cost came into it, i could have bought much smaller relays but these Tyco ones were the cheapest that would do the job. As it is they'll carry 10 amps so they're well overrated, and another benefit is around 1,000 volts worth of isolation between the coil side and the contacts. happy wiring!