Well that's... odd. It seems to be working now. I failed my first attempt at the map I'm working on, so I started again from scratch later yesterday evening. I had removed the mod from the active list, but after putting it back in now to show you guys, it works. Priorities are saving properly.
I have no idea why it wouldn't have worked before, yet does now.
I have no idea why it wouldn't have worked before, yet does now.