It seems that disabled flags (Those that are automatically disabled on the first placement of a stone) are randomly enabling after server restarts. It only happens with stones placed before the restart. I'm using the latest dev build and the latest Spigot build.
EDIT: Changed some of the info, I figured out that if I /ps toggle a flag, then restart, all the flags stay the way they were before the restart. It only enables all flags after a restart if I don't toggle any flags beforehand.

My config: http://pastebin.com/KhvkSRS6 (Home Protection and Town Protection are the ones in question)
Server log: http://pastebin.com/j56CHXdD

Also (This is a bit unrelated), is there anyway to update existing fields with new flags? My players' existing fields aren't updating with new flags after I added them to the config.