When the boards are configured as left handed, seq_l works perfectly, including fluxtest, CC16 and pushbuttons/LEDs. Have not tested the OLEDs in this config, I will however.
When the boards are configured as right handed, with seq_r loaded only the pushbuttons/LEDs on the JA board work. LEMEC pushbuttons do not trigger the LEDs, and produce random lighting of the keys. CC16 doesn't have an affect on the LED matrix. With OLEDs connected they are blank.
Is there anything else you can think of which would cause LH configuration to work, but RH to not work?
I will check everything you mentioned. Thank you.