I had that bug too. Fixed it this morning, actually.
It happens because all the achievement details get duplicated everytime you resign. So after a few dozen resigns, it'll take many minutes to load the game.
First of all, go to Paradox Interactive\Europa Universalis III\achievements\achievements.txt and just delete everything that's in the file. Don't delete the file, delete its contents; you'll have an empty achievements.txt. Save that.
Then open the savegame you want to, well, 'save'.
They're in Europa Universalis III\save games. Open one with Notepad. This took me... Fifteen minutes? Half an hour? Anyway, feel free to go do something else. Notepad is working, it'll open the file, but it'll take
long.
Once its opened, Ctrl F nr=". Put your cursor in front of the first nr=", move to the bottom of your file, and shift click at the end of the last nr=". Delete all that (might take some time too).
If I remember correctly, there's a weird string of numbers and letters at the very bottom of the file. You can leave those; I didn't delete them and it works fine. You should check whether the }'s close correctly though (maybe you have to remove one, I don't remember).
Anyway, save your repaired savegame, and go play!