is it the issue on github mentioning not being able to read the switch matrix? if so, have you tried to read the io pins yourself without an additional library to see if they do as you would have expected?
Libre Hardware
Thats the issue, yeah. I haven't manually read the pins yet, but I just found something strange.
I connected an LED to one of the column pins to see whether the MCU was sending scanning voltage, and it was. Then I put it in parallel to a row pin to see if the switches were returning that scanning voltage when pressed, and they were. Then I noticed that whenever I added the led to a row pin, the serial monitor showed keypresses for all the keys on that row, and the inverse when I removed the LED.
So, apparently, this whole time the key matrix library has been designed to work with a pull down resistor rather than reading return voltage. My whole PCB is modeled after mechanical keyboards, so it was not designed for pull down resistors. Now I must rewrite parts of the library or find one meant for a keyboard-style circuit.