Hm... I took a look at your xf86config file. From the first look of it, it appears to be ok. But a couple of questions arise.
1.) Are you sure that this file is the one used by XFree86 when it starts? You can verify this by taking a look at /var/log/XFfree86.0.log. grep through it with this command:
grep "Using config file" /var/log/XFree86.0.log
This will present you the full path of the config-file XFree86 uses.
2.) Do you explicitly select any of the multiple server-layouts defined? Or is it just started as is?
If that config file, you posted, is actually used, you could try any of these commands to select a particular layout (from the command-line):
X -layout AGP
X -layout PCI
X -layout Both
X -layout AGPTwinView
X -layout BothTwinView
See if any of those work. If you don't use the -layout option server-layout "AGP" will become the default one and get used.
3.) Did you write that xf86-config file yourself or was a special tool used?
4.) Did you check /var/log/XFree86.0.log for any error messages or strange entries?