Pete,
Firstly, if you are using mechanical limit switches it my be worth just tapping the side of each one lightly with a small screwdriver handle (or similar) and seeing if this causes the 'limit switch activated' - switches can sometimes have loose or bad internal contacts which could be activated by vibration. Also, it would be worth checking all your limit switch wiring, connectors etc. for damage or poor contact (I am assuming you are using 'shielded cables' for your limit switch wiring - if not then you should be).
Secondly, try increasing the Noise Filtering values in your SS Config Dialogue.
Tweakie.