I'm making an assumption in the title because I could just be missing something, but setting an output index to something like 'signal-red' will not color the lamp it's connected to. Immediately switching the lamp's input to a vanilla combinator instead will cause it to light up properly, ensuring that the condition on my lamp is set up correctly.

output["signal-red"] = 1 works for me..
lamp is set to anything > 0

Really? That's interesting; I'll have to try that again. I ended up doing this which works for the time being.

combinator.get_control_behavior().set_signal(1, {signal={type="virtual", name="signal-green"}, count=80})

Just tried the simple way like you mentioned (aka output["signal-green"] = 80) and it still doesn't work. Interesting... not sure what would cause that.

It must be another mod apparently. I tested with only LuaCombinator3 and it worked. I'll have to check which one it is.

I've no idea which one it would be, because testing every mod loaded/unloaded in a new world works just fine. However, my original save in which I want this functionality still doesn't have the lamp working correctly. Some mod must have tainted it somehow in this save only, because otherwise it works in a new world.