Sorry, I was wrong about the USB power. The external 12-24V is necessary for the inputs and the 0-10V PWM. I don't have my CNC near me, but looking at the manual of the BoB it seems to be the case. If the 12-24V is not connected then the inputs are not sensed or will give random readings.
Have a look at the manual, perhaps it helps you out with your problems. This BoB and the UC300ETH or UC300USB are pretty easy to install and configure in Mach3 and since you managed without the BoB it should be pretty straight forward with the BoB.