There is an easy way to update your PB version.
You need a rcon tool like procon.
1. Go to the punkbuster tab.
2. Type "pb_sv_update" in your console (without the quotes), press enter and waite until the update is done.
3. Restart your server with "pb_sv_restart"
4. I´ts done, the PB version should be up to date now.