It should automatically. When you uninstall, it will ask you if you want to remove the library files and the settings. There will be two checkboxes so that you can choose one, the other, neither, or both.
Be sure to keep your library. The library is the database of all your media, but not the media files themselves. This includes all the playlists, view schemes, and groups in the tree, as well as the "entries" for the individual media files.
In your case, I would have it clear your settings. This includes your toolbar buttons and preferences, however, since you are having a very odd issue, I'd let it put these back to default.
So, to review...
Keep the Library files. Lose the settings.
Then reinstall. Make sure to get the most recent build. This is 11.1.201 (which Jim linked to above). You can always find the download for the newest build by coming here (to the Interact forums) and opening the Media Center 11 board. The newest build will be posted in a "sticky thread" near the top of the first page of the board. In this case you want the build that's listed as "This latest build (usually safe) of MC11.1 is here". Build 201 is fine, you can go ahead and use it.