ipatch:
So I found the schematic for the shield I have, it is the kegboard-mini, and the schematic can be found here -> https://github.com/Kegbot/kegboard/blob/master/hw/kegboard-mini/kegboard-mini-board.pdf?raw=true
That's not the schematic. That's a couple layers of the board layout showing component outlines. That schematic shows how the components are wired together:
The schematic shows Arduino Pin 2 (D2) going to "FLOW-A" which has a 2.2K pull-up resistor an is then connected to pin 6 of the two RJ connectors. To control the FLOW_A LED you have to use Pin 4 (D4) instead.