Obviously there is something wrong here,, in device manager you should be able to go into display properties and see a drop down line that displays the names of BOTH adaptors,, if you dont see this, then one is NOT being loaded,,,
delete the AGP,, remove the card,, reboot the machine,, let it see the onboard video,, load the drivers and install,, check properties to see if it is in Device Manager,,
Then shut down,, put AGP back in ,, load drivers,, then check device manager , display properties again,, you should be able to see both of them,,
then ,, ensure that "Extend to ...." is checked off,,
this sounds like an error in process,, not hardware,, or OS,,
cheers,