I'm having the same problem. Right now I have the PCIe GPU enabled in BIOS and multi-display disabled. Windows installed the AMD driver itself. If I install Catalyst I start having problems (ver. 12-10) Originally I had my computer working with both GPUs and Virtu MVP enabled. But even then I had problems with Windows (7, 64 bit) suddenly freezing and the black screen of death. No video. Only a hard reset would resolve. I even returned my Sapphire HD7970 card for RMA exchange, but this new card already did the same thing when I was trying to install Catalyst.
My solution right now is to only use the PCIe GPU with the windows installed AMD driver. So far it has been stable with no glitches.
I have never found a good explanation of how to deal with the Catalyst drivers and the Intel HD4000 driver.
When I reinstalled the replacement GPU, Intel HD4000 was already installed, and the latest update working fine, without any incidents the whole time I awaited my replacement. (about a month) But installing the latest Catalyst after installing the GPU caused all sorts of havoc with Windows 7. I tried all sorts of installation and reinstallation options, but nothing seemed to work.
In device driver, if I have the PCIe GPU enabled in BIOS, I will see just the one driver "AMD Radeon HD7900 series" If I check with just the iGPU enabled in BIOS, it will show BOTH display drivers, the "Intel HD4000" and the "AMD Radeon HD7900 series" driver.
More ideas: Turn off the Windows Driver update/install, then install the drivers. First the Asus provided Intel driver, then reboot and install the Catalyst driver. Reboot then turn the Windows driver updates back on.
I just don't have time to devote to this right now. I want to get some work done, and I just can't keep playing around with the GPU drivers, trying to get them to function properly. Obviously SOMETHING is causing conflicts that are catastrophic to Windows and the GPUs themselves.
Asus Maximus V Extreme BIOS 1903, see specs above avatar.
Asus G73 jh A1 laptop, BIOS 213, vBIOS OD2, 8 GB Ram, 240 GB Intel SSD, 180 GB Intel SSD. Win 7 Pro. Purchased new from PowerNotebooks.com in May 2010.
(both have 1920X1080 hd screens, mine above, hers below )
Asus G73 Sw XR1 laptop 8 GB Ram, 160 GB Intel SSD, 80 GB Intel SSD. Purchased used >Ebay 1/10/13, Did clean install of Windows 7