I have an ATI graphics card with an AGP connection and a DVI port, and an Intel graphics processor on the motherboard with a VGA port. I have two monitors.

When the graphics card is unplugged, I get this from lspci:

00:00.0 Host bridge: Intel Corporation 82G33/G31/P35/P31 Express DRAM Controller (rev 10)

00:02.0 VGA compatible controller: Intel Corporation 82G33/G31 Express Integrated Graphics Controller (rev 10)

When it is attached, I get this:

00:00.0 Host bridge: Intel Corporation 82G33/G31/P35/P31 Express DRAM Controller (rev 10)

01:00.0 VGA compatible controller: ATI Technologies Inc RV380 [Radeon X600 (PCIE)]

01:00.1 Display controller: ATI Technologies Inc RV380 [Radeon X600]

Note the absence of 00:02.0 - this is apparently causing the VGA monitor to say "No Signal" and the only the DVI display to show up in the list.

I checked for problems in xorg.conf... there isn't one. I have no idea how to build one.