Found out something interesting back when I was emptying some events to set up a party changing system.
If you clear enough events of commands, it seems the data that dictates whether chests are closed or open gets moved slightly, causing some unopened chests to be open by default.
On some maps it'll be just one random chest open (Baron Castle Lobby, Damcyan Treasure Room) while on other maps ALL chests will be open (First map of Mt. Ordeals).
Luckily, once enough commands are added to said empty events, this issue fixes itself! Just don't go and empty every event in the game if you're starting a new project haha.