You can use the keypad to move towards the switches, just that once the the prox switch senses the target and stops movement, subsequent attempts with the keypad (arrow keys), will move past the target.
What do your input lights look like when away from the target and the LED on the prox is on.
I'd double check the wiring for the prox, e-stop, and even the zero plate. I'd also reset to the defaults for your machine with a UR to be sure that you have the VN settings at default.
If your limits are set to 'Off', they will not work with the keypad or with a file. If file limit checking (different than limits off) is off and limits are on, keypad moves will be stopped by the prox switches but not files.
It's possible that you could have one or more bad prox switches.