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We need more info:

* Verify exactly which DLCs are working and which are not. Do they show in the launcher?
* What OS are you using?
* Check your DLC installation folder (normally "Program Files/steam/steamapps/common/Crusader Kings II/DLC"). Do you have files there called dlc007.dlc, dlc007.zip (Sword of Islam)?
* If not, check the same in the folder "My Documents/Paradox Interactive/Crusader Kings II/DLC".
* Are you using a custom 'userdir'?

Also, please give us your logs (under "My Documents/Paradox Interactive/Crusader Kings II/logs")
 
As Doomdark says; we'll need more info.

We've tried to reproduce this with our QA steam accounts; with Ruler designer, Sword of Islam and Legacy of Rome installed, all three work just fine.

one thing you might try, beyond the information Doomdark mentions; try removing or renaming the dlc_signature file (in "My Documents/Paradox Interactive/Crusader Kings II"), see if it recreated correctly.
 
Does it specify anything about what new content is supposedly available, or just "new content"?
 
Ok, just a random thought:

Do you start the game with a shortcut? Could you possibly have set the wrong working directory for the game, perhaps pointing to another installation?
 
Same as Arimahn, excepting I didn't buy Legacy of Rome yet.
I am playing the game on Steam, Win7 64bit home, and since the update today, my DLCs, although showing up in the launcher, don't seem to work in-game (the 2 easiest to verify are the ruler designer and Sword of Islam, both are telling me I don't own them in the tool tips on the province selection screen).
I tried unchecking them and checking them again, but it didn't make a difference.

I tried deleting the DLC signature file : it is created again, with the exact same string of characters inside it.

Thank you for this most wonderful game, and I hope I can get it running again in all its glory again soon!

did you fully quit steam at some point? if not, try that (it has helped for some people at least)