Do a continuity test with the relay boards. Bypass should give you contact between Pin 2, 3 on the input and respective pins on the output XLR and engaged should not, as you know. Verify that then maybe the next step is to bypass the transformers and go straight in and out of the PCB. Also verify that signal is present at the input header of the main board. Also you could wire an XLR straight to the board with no relays. You may have already done all of this but it seems that this is one of those cases where you get to start over and stare at the board until you see the problem. I've been where you are in the troubleshooting process and it sucks.
Thanks!
Paul