Electrical noise is causing the limit switch triggers. You can increase the debounce setting in General Config to see if it helps. Try setting it to 2000-5000.
Your sure they're disabled in Ports and Pins screen?If the home switches are not enabled, when you hit reference it should zero and home to it's current position. Mine does not. It will still activate the motors and try to find a home switch.
Do you have one switch or two? If only one, then check "Home Slave With Master" in general Config.
Also, I have my A axis slaved to my Y on my gantry. When I hit reference only one of the motors turns and puts the gantry into a bind.