Something is pulling the voltage down. it can be anything on the 5v rail, which includes the controller cpu, throttle, PAS, motor hall sensor, motor cable and any other cables. That only leaves the battery. If you unplug everything from the controller except the battery, and the 5v is still down, it has to be something in the controller. If you look at the PCB, you'll find that all the 5v wires go to the same area. have a look around there to see if anything is amiss.