I reimplemented all my settings one by one, each time closing and reopening the program. I also logged out and back in a few times for good measure. All my settings are reimplemented now including the extension and everything still works just fine. I don't know what happened before but it's all fine and dandy now.
I was able to clear all settings with the following commands.
gsettings reset-recursively org.pantheon. scratch. settings scratch. saved-state
gsettings reset-recursively org.pantheon.
I reimplemented all my settings one by one, each time closing and reopening the program. I also logged out and back in a few times for good measure. All my settings are reimplemented now including the extension and everything still works just fine. I don't know what happened before but it's all fine and dandy now.