Should work, just remember to use the correct SEQ HWCFG file. Like the .NGC, the left/right suffix refers to the position of the JA board. You can also add boards one by one for the _NG testing, good idea.
It would even be possible to make a custom .NGC based on the _R file and adjust the shift register addressing to test lemec _R first in the chain. You need to adjust the positions of the shift registers because there are three extra ones (that go off to the JA matrix) before the "main" BLM and encoder scanning ones.
Maybe some cables are twisted? They should run in a nice chain, correct? Do all of the IDC shrouded header notches have the correct orientation?
You might consider reformatting the SD card or reflashing the app.