Can't help you with the Linux part but it sounds like you have the Primary Video Port set to Auto in the BIOS and/or the Secondary Video Port set to something other than "None". Set the Primary to HDMI and set the Secondary to NONE. You'll probably also want to enable HDMI/Display Port Audio under On-board Devices > Audio.
The BIOS has been set to allow me to define the primary and secondary ports manually. And I have set the primary to HDMI and the secondary to DVI-Analog
I just did a live chat with Intel tech support and the guy I was talking to it on it said that for the splash screen to come out on the DVI port regardless of the BIOS settings was correct behaviour. Sounds more like a BIOS bug to me. Basically there is ONLY an HDMI and a DVI port on the back of the board, so I have no way to drive a modern display which I want to be the primary and an old VGA only display as secondary.
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Okay, it's doing what you told it to do. If you want the primary and only boot output to be HDMI, the Secondary needs to be set to NONE.
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Keep in mind that the BIOS options are for boot only. If you want the boot to appear on the HDMI port, set the Primary Video Port to HDMI. If you don't want the boot to also appear on another display set the Secondary to NONE. You're telling the BIOS you want dual boot displays if anything is defined in the Secondary. I can't make it any clearer than that. After booting, the OS will still use any display you have connected to the motherboard and you can define the VGA as an extended display (at least in Windows).
I understand what you are saying, but I don't think it is working in practice.
Certainly even though I have set the secondary output to NONE, and the primary output to HDMI, the splash screen is appearing on the DVI-A monitor!
Linux's Xorg Intel Driver seems to be using these values for something. It appears to be reflecting these changes in the BIOS to how its is operating.
I just managed to get a pretty well perfect setup for it, but I then tried rebooting and I have lost it all again.
Finally got it working - this splash screen is wrong, but that is a small price to pay.
BIOS is set for primary HDMI secondary None - but still the splash screen comes up on the VGA port
I set the Linux stuff up in /etc/X11/xorg.conf thus:
Identifier "H67 Integrated Graphics"
Option "Monitor-HDMI2" "Iiyama 24in"
Option "Monitor-VGA1" "Iiyama 17in"
Identifier "Iiyama 24in"
Option "PreferredMode" "1920x1080"
Option "Position" "0 0"
Identifier "Iiyama 17in"
Option "PreferredMode" "1024x768"
Option "Position" "1920 0"
Identifier "Default Screen"
Device "H67 Integrated Graphics"
Monitor "Iiyama 24in"
Modes "1920x1080" "1024x768" "640x480"
And this gives me both screens visible! with the 17in monitor positioned to the right and with the top edges aligned.
I was just trying to duplicate the HDMI Primary and hung my system. (I have the same board.) I know you have to boot after making the initial change but I happen to catch the system in a Defrag. Windows 7 didn't like that at all. I was stuck with NO display and trying to re-power. Ended up having to re-configure to get to the BIOS and set everything back and let Windows recover. So, I'm back and leaving everything as is. Anyway, glad you were able to get the displays working. I think you're right about a bug in the BIOS.