In order to see if it is enabled, you should run the following command:
cat /boot/config | grep CONFIG_AGP
If it is set as y, you have to recompile your kernel. If otherwise it is set as 
m, you could insert agpgart in cat /etc/modprobe.d/blacklist. Next reboot it 
shouldn't be loaded (you can verify it with lsmod | grep agpgart).

-- 
Gnome 2.16 crashes after loading some apps
https://launchpad.net/bugs/65971

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