Hmm, I doubt this would be the origin of the issue since it usually doesn’t impact custom commands, but make sure !commands is set to everyone and enabled as well.
Just guessing around to try to find where the issue could be at this point…
Also, I felt like it wasn’t necessary to give you this link since Nightbot was responding in your chat, but have a look here if you haven’t already, we never know: Nightbot Troubleshooting