Reflowed the ttasnsistors on the top side and now I am back to 12 LEDs on. I'm assuming the LEDs shouldn't be on, but otherwise that feels like an improvement as it means I get mattias switch events for 12 of 16. I'm also getting events for depresses on the right 4 encoders although they seem a bit random in the actual event details.
I've also replaced IC2, IC3 and T3 based on advice from ChatGPT but that made no difference.