You would be better off contacting them and explaining the problem. Since they've just replaced the motherboard, it is their responsibility to ensure that the repair is satisfactory. I would expect all ports to be in full working order upon its return. It could be nothing more simple than the repair technician omitting to plug the USB lead into the motherboard header OR it could be a fault with the new motherboard. Either way, my advice would be to contact them to see what they have to say.