@FelixUCF which version 6HC board do you have?
The 5V_ext supply on the IO_ connectors of the 6HC is derived from the main 5V supply through a diode. Older 1HC boards that do not support 48V VIN also have a PTC fuse in that circuit. The 5V_ext voltage on the IO_ connectors will be missing if either the diode or the fuse is open circuit.