I had free version 2.4.5 then bought paid version 2.6.1 but everytime the server restarts it goes back to the free version and i have to delete everything and reinstall it.  And then never server restart it goes right back. 

sounds like you need to blacklist raidable bases in your Automatic Plugin Updater as it cannot revert by itself

The server host i use has a mod page that uses UMod and i forgot to delete it from the list so every restart it uploaded the free version. But i got it fixed it now.