My first thought is that the display config file may have become corrupted somehow, and it isn't being properly cleaned up between installs for some reason.
The first thing that can be tried is entering developer mode on Steam Deck and clearing the Proton cache. BE WARNED - this might remove saved games (you should be able to restore them if you have Steam Cloud enabled, so make sure you have).
To do this, make sure the Deck is in Developer mode (Settings > System > System Settings > Enable Developer Mode) then you can go to EotU's Settings (gear icon) > Developer > Delete Proton Files.
You can manually back up your saves too by navigating to this folder in Desktop mode, and copy-pasting the saves somewhere else:
/home/deck/.steam/steam/steamapps/compatdata/463530/pfx/drive_c/users/steamuser/AppData/Local/EotU/Saved/SaveGames
A more targeted and safer but more fiddly option is to just delete the engine config files, which might work by forcing the game to rebuild them. Theyre in:
/home/deck/.steam/steam/steamapps/compatdata/463530/pfx/drive_c/users/steamuser/AppData/Local/EotU/Saved/Config/WindowsNoEditor