Hi @coanderson,
The ArduSub firmware recently got some updates to how it handles lights configuration that QGC doesn’t know about. I believe QGC should still be capable of performing the old configuration approach, which the firmware should then auto-fix on the next reboot, but when that fix happens the QGC Lights page will again present the lights as not configured.
The joystick button functions have not changed, so as long as the relevant buttons are assigned they should still be able to control the lights, and the lights percentage should still be reported. If that’s working in Cockpit then it should also be working in QGC, but it’s possible your joystick configuration is not the same between the two software (which might be the actual cause of your issue).