Try manual updating
PunkBuster Online Countermeasures
you can also try
1. Visit and download Punkbuster Updater at -
http://www.evenbalance.com/index.php?page=pbsetup.php [evenbalance.com]
2. Run the pbsetup.exe file, choose I agree.
3. Choose Add a Game > Battlefield 3 and click on Add Game.
4. Click on the Battlefield 3 name and click on "Check for Updates"
5. Allow Punkbuster to update the game and respond with "All versions are up to date."
6. If you wish to confirm, the section client version should state (v2.279 | A1386).
Server Owners
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1. Please contact your game server provider to ensure you have the latest updates!
2. If you have rcon access try running the command:
!pb pb_sv_update
3. Please allow 30 minutes to an hour to update punkbuster. If you are unable to update punkbuster, or uncertain if the update has succeeded, contact your game server provider for support otherwise continue on.
4) Run the commands below separately in the order provided.
!pb pb_sv_restart
!pb pb_sv_ver
The server should reply with the below after !pb pb_sv_ver:
PunkBuster Server: PunkBuster Server for BF3 (v1.826 | A1386 C2.279) Enabled
PunkBuster Server: Game Version