When you restart or reload the server, the config.yml gets reset. Unless I am being completely stupid.

The config.yml should not be resetting, make sure you have the latest version, also to update the config.yml do /lsreload

Oh also send me the console logs

Nothing is put in console all that happens is that when I restart or /rl confirm the config resets.

Edit: Just checked I am on the latest version. Also here is my log when I reload, it still reset the config.
latest.log

do not use /rl confirm, that is bound to break things, use /lsreload to reload only the plugin's config and recipes, if it works great, otherwise i have no clue what you have done

Okay thanks