I have finally got round to putting home switches on my machine, but have a problem with the X and Y axes activating the Estop rather than homing. The Z axis seems fine and both the X and Y axes light up the led's on the diagnostics page. The actual Estop also works fine. Any body got a clue whats happening?

Sounds like electrical noise, you could try setting a Debounce Interval of 2000 and see if that helps but best idea is to shield and properly ground the wires if you have not already done so.
Hood

Thanks Hood, that got it, all is now perfect!!!!!