There are some reasons why you keep getting the bug.
One, the bug is actually getting cleared by reinstalling but is getting reintroduced by 3 possible things.
1. Player action. Unlikely if you experienced the bug immediately after uninstalling/reinstalling properly.
2. Bug is inherent in the client build. Possible, but not everyone experiences it.
3. Reintroduced after uninstall/reinstall by the server. Servers have authority over clients when it comes to settings and such most of the time. If this setting is stored on the server so that you can use it from computer to computer, then this is likely what is happening. All you would need to introduce this bug is that the part about saving your preferences to the server is no longer working, meaning that you can never overwrite the preferences you had when this function was working.
Client asks the server for serverside user preferences
Server sends them to the client
Client examines and says, "Aha, you want to autojoin."
Client pops up the client with the settings it thinks you want based on the server.
There is nothing wrong with the way this is designed. It's actually beneficial, because it means you don't have to reset your configurations when you play at a friend's house, but it really sucks when you have a bug like this.
I will look into a fix for this.