In standalone emulators too? The fact that they’re lighting up, I’m assuming individually means that it isn’t a connectivity/hardware problem.
My guess is, the Retroarch config needs to be overwritten for compatibility, and the L and R buttons haven’t been defined yet.
Otherwise test things out, using this.
I haven’t done the 0.4-0.5 upgrade, but can say that a fresh 0.5 image does indeed work with the light key.