What causes Link2SD to not automatically link apps? When I install an app from the Play Store, Link2SD doesn't automatically link it but if I go to the app manually and press Create Link, it works and the app gets linked. It just won't do it automatically. I already tried recreating the mount scripts multiple times.

Already tried changing the mount script to either Ext2 or Ext4 but they both gave me an error which ascertains that my 2nd partition is in Ext3 format.
There is option in settings ( auto link apps)  check that option. Your apps will be linked automatically after install.