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There are at least three reasons, why the checksum could be different:
  1. One of the files in the eu4 installation got corrupted/was changed
  2. There are additional files in the eu4 installation folder
  3. a mod is active for some reason(the eu4 folder in Documents can override game files)
A few things that you could try if you haven't tried them already:
  • verify the integrity of game files in steam
  • clearing the download cache in steam and verify the integrity of game files afterwards
  • remove all mods and unsubscribe from them in steam. Remove also mods which should be compatibly with achievements. Also remove custom mods that you didn't install via steam. (You can move them to a completely different folder if you don't want to delete them). If this fixes your problem, you can activate achievement-compatible-mods again one by one to see which one is causing the issue.
  • move the folder "Paradox Interactive\Europa Universalis IV" from your Documents folder to some other place. You could also delete it, but then you lose all save games and screenshots which are stored there.
  • find out where steam installs the game and any mods on your computer. Then uninstall and verify that these folders don't exist anymore. Sometimes files get left there even if you uninstall
  • A few people have reported that uninstalling eu4 and uninstalling steam helped(but I don't think that this does anything more than the previous options)

Disclaimer: I'm not working for Paradox. I'm just trying to help people.