I recently updated Doomsday from 2.0.3 to 2.1.1 version (same folder), on Windows 7 x64.
First time I loaded 2.1.1 version, a "Fix" option appeared, so, to fix it, I had to reload all stuff (textures/models/ui/music) for each game.
P.S.: the addons folder remained untouched, since I've only updated Doomsday version running its executable (msi 64 bit): this means that all stuff (textures/models/ui/music) is exactly the same as 2.0.3 version (I have a backup copy of that folder, containing WAD, PK3 files and *.BOX subfolders, and it's identical).
But, despite this, now I can't load 2.0.3 savegames due to this error: