You can try deleting the PB folder from the game installation, Then run PBSetup and let it check for updates. Make sure you don't run PBSetup from inside the PB folder cos using this doesn't seem to work.
You can update PB manually here is a small guide how to do it someone else was having trouble after the recent BF3 update.
looks like your not getting the AUTO PB update... (config issue on your end)
Try a "repair" out of ORIGIN on your BF3 install
Go here http://www.evenbalance.com/index.php?page=dl-bf3.php
And do it manually
Get the correct file, then follow the instructions below
" To Manually update your local PunkBuster Security Files, choose "Save As" from your Web Browser's "File" Menu and explore to find your game folder and the subfolder called "pb". Save this file in that location ([game path]/pb/pbsec.htm or [game path]/pb/pbsecsv.htm). The next time you start your game, your PunkBuster will have the latest security information necessary to accept auto-updates from PB Servers."Edited by AlvoAsh - 11/30/11 at 5:39am