UPDATE: The camera app froze on me once again (still on the 10-12 nightly) and the phone rebooted by itself. When I unlocked the phone after it had rebooted, I saw text that said "Capacitive buttons brightness has been granted superuser permissions." Then, it shut off the capacitive lights like it should at boot. However, right after they shut off, they immediately came back on. So I believe the app is shutting them off initially (which is the option I have selected; also, it gives the "granted superuser permissions" text), and then somehow they come back on. Hope this helps! I'm still trying to man up to get that logcat haha.
Did you by any chance flash Turge's MOD to set the capacitive button brightness: link? If you did then my app and his MOD would be "competing" to set the brightness on boot.
Also, let me know if there is anything "blocking" you from capturing a logcat. A logcat is the most standard log captured by Android developers and is an incredible tool for debugging problems just like this. If you're concerned about posting it publicly, you could even PM it to me.