I'm using 'HD Graphics 1000(GT1)' on 'ECS H61H2-M2' motherboard.
And, I have same 2 monitors to use for dual monitor.
I upgraded graphics software but can use only 1 monitor..
Intel® Processor Graphics 2000 (ver 188.8.131.5256) on Window 7 64bit
And, on 'Intel Graphics and media control panel' - graphics properties - Display - Multi Display
I can see 'one option' only at operation mode, can't find clone or multi display options.
I suggest you to test using a different monitor in order to see if in fact the issue would be related to having two displays of the same model and update the BIOS of your system. Also test with the latest driver that is provided by your computer or motherboard manufacturer, not the generic driver on our site and see if the issue persists.
In addition, please define what video ports are being used and if there is any adapter or converter being used in between.