I've not slaved the 2 side together yet just so i can confirm each side is working correctly. I've no tightened things up yet so there's enough slack in the gantry to allow independant movement of each side.

The pendant plugs directly in to the BOB, not the PC so commands as different and with this working i though jogging via Mach would be fine.

Well it turns out that the pendant does conflict with keyboard jogging commands. If i unplug the pendant it it's fine and both side jog via the keyboard. They're now slaved together and all is good in the world for now and i can tighten things up.