We have never used CBB-Serial Cape before. Coud you please check if the way 5V_VDD works in BBG be the reason In CBB-Serial Cape scehmatic 5V is powered by 5V_VDD (which is not available in BBG due to lack of DC Jack port)
BBG pins works like BBB. Refer BBB System Reference Manual :
"VDD_5V is the main power supply from the DC input jack. This voltage is not present when the board is powered via USB. The amount of current supplied by this rail is dependent upon the amount of current available . Based on the board design, this rail is limited to 1A per pin from the main board.
SYS_5V rail is the main rail for the regulators on the main board. When powered from a DC supply or USB, this rail will be 5V. The available current from this rail depends on the current available from the USB and DC external supplies"
There is no DC input jack in BBG. Hence, VDD_5V is not present. Please refer BBG schematic for more details. There is a way to connect SYS_5V to VDD_5V by using a 0 Ohm resistor.
Thanks and Warm Regards.