If its a limit or watchdog issue you should see an error in the status window, so if you are not it sounds like it may be something else. However try 500 or so for the debounce interval and see if that helps. Often people go as high as 2000 or more but as you are only having occasional problems 500 should be plenty if it is noise thats the issue, but as said if there is no error message it sounds unlikely.
Oh are you using the parallel port or an external motion controller?
Hood