Okay, now the game is completely broken. A day later, and to all my inputs are mapped to me interacting with other windows. Maybe its something to do the engine, me trying to force the Shrine to happen last night, an error in the most recent version, or I just pressed a wrong key at some point, but I'm going to delete my current copy and report back if/when this happens with the new one.
So it didn't get fixed by deleting it, so if anyone know how to fix RPG Maker 2003 after it starts to only respond to you interacting with anything but the game, that'd really help me out.
EDIT: Okay, it's fixed. I don't know how I did it, but I did. I'll report back if the RNG on the Shrine event is still bad