I am having a similar problem. I recently purchased an Optiplex 3010 with the onboard Intel HD graphics chip with VGA and HDMI outputs. When I plug in a VGA and DVI monitor, using a HDMI/DVI adapter, the display flickers between these two monitors. It acts very erratically. I am able to change the settings in the media control panel to clone the monitors but the settings won't stick. I have updated the graphics drivers, the bios, and the chipset and that didn't help. i got Dell involved and they simply concluded that it's a bad motherboard. They said they would send me a replacement mobo. I don't know if it's. worth the trouble. Has anyone got this to work even?
We have several of these at my company. Almost all of them are using the dual monitor setup. Just recently, i have one start to have an issue. We are using the exact same setup with one VGA and one DVI using the DVI-HDMI adapter that was included with the optiplex system. This worked for some time and then suddenly the DVI monitor was not being recognized by windows. Upon a reboot., i noticed that the DVI monitor showed the BIOS screens and the windows boot screen. However when the logon screen for windows appeared it was on the VGA monitor. I tried installing a brand new video card but it would not even recognize the new video card existed, only the onboard VGA.
So i reconnected to the onboard video sources and then tried disabling and then enabling the onboard video through device manager. Voila! The dual screen setup returned just as it was to begin with, with the extended desktop on the second monitor. However upon reboot, the system reverts back into only recognizing the VGA monitor until the video has been disabled and then enabled again. This is the current state of this machine. I have told the user not to reboot until i can find a real solution. If i cannot find one, my next step will be to contact Dell and see if i can get a warranty replacement.