Hi cwathen,
Have you carried out a FULL virus scan recently?
Re-installing the utilities as suggested in a reply to your previous post should reinstate both the Fn key functions and Vaio Control Center, but you could possibly have other problems.
If a Virus scan followed by re-install of the utilities has no effect then maybe you should consider a return to factory defaults using either the HDD recovery utility or your recovery disks.
Be aware that you will lose all personal data if you take this route so backup all data you need...
Rich