Since you have an onboard device as well as a card, make sure that your "[Device]" sections have a BusID: entry.
There is an xorg-X11-man package you can install for the xorg man pages.
Code:
BusID "bus-id"
This specifies the bus location of the graphics card. For PCI/AGP cards, the bus-id
string has the form PCI:bus:device:function (e.g., "PCI:1:0:0" might be appropriate
for an AGP card). This field is usually optional in single-head configurations when
using the primary graphics card. In multi-head configurations, or when using a sec‐
ondary graphics card in a single-head configuration, this entry is mandatory. Its
main purpose is to make an unambiguous connection between the device section and the
hardware it is representing. This information can usually be found by running the
Xorg server with the -scanpci command line option.
My guess is that you either don't have BusID entries in your xorg.conf file or that they are switched around and the busid entry is causing the wrong device being used.
Read your xorg.conf log. It will probably indicate what the problem is. Also post your xorg.conf file.