Pretty straight forward. The config file resets to default values when checkforupdates and oxide.reload PluginUpdateNotifications is executed. 

I think you need a statement (line 55) so that it doesn't create a new config every time. 

Which part of your config is getting reset? The config gets upated with automatically blacklisted plugins each update check if you have automatic blacklisting enabled.

It looks like I had some server side issues that was causing this. My SFTP was acting up. I'm sorry for wasting your time. 

All good dude