Erm ok well the PlayStation controller and it's plug-in is a prime suspect because it probably handles the E-stop as well, but I've never used one so not sure on that.
If it was me I'd be disabling the PS controller plug-in to verify it's not this.

However, try this first and see if you get movement. Go into ports n pins then Inputs and look for E-stop. Change the Active Low to the opposite of what it's set to now. ie If a tick toggles it to an (X).

This is basically by-passing the E-stop and tricking Mach3 into thinking it's working, so be careful because you effectively haven't got a E-stop.

If this works then it's either something on the E-stop wiring (or the BOB as blown an Input) or the PS controller or it's Plug-in are broken.

Without knowing a little more about wiring and you tracing wires etc then it's hard to say for certain.