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How did you fix it?

For the flags, try deleting documents/paradox/ck2/gfx/flags/ folder and let the game recreate it.
 
Game crashes whenever I click on a CoA ... :-( (with Jade Dragon, no mods)
This is quite unrelated to the topic of this thread ... however try a full **clean** re-install:

- move any valued save games elsewhere
- "uninstall" in Steam-CK2
- manually delete both the Steam/SteamApps/common/CK2 AND Documents/Paradox/CK2 folders
- re-install game in Steam, run a Steam Verify when done.
- start the game with no mods active and test

In particular make sure there are no files or folders left under either the Steam CK2 or Documents CK2 locations, before installing again.