Matt:
As it happens, i just installed limit switches on my X axis. While I was debugging it, I connected the switches to the parallel port with a piece of unshielded cable, and clip leads at the switches. I had to set my debounce to 10,000 for the machine to stop tripping randomly.
Once I figured out the wiring, i replaced it with shielded 22 gauge cable, and the problems went away. i think I have the debounce down to 300 now, and i may try to see how low I can reliably go.
So if your limit switch wiring is not shielded, you may need to change it out to shielded wiring. If you do, make sure you ground the shields to the parallel port ground.
Andy Wander