I've not seen this problem and using the same board but with an i7 3770, I have a DELL 24" monitor connected via DisplayPort (1920x1200) and a second monitor via HDMI to DVI.
It's strange you should see the problem while windows loads the initial graphic animation as at this point the monitor drivers aren't loaded as far as I know, which would suggest not a driver problem.
What does spring to mind is 1920x1200 is the top resolution you can get with a DVI single link that these boards support, so you need a good quality DVI cable and adapter. I'd suggest changing the DVI cable to another one to see if that helps, even if the cable worked previously, as it is worth ruling it out.
One oddity I've seen in my case is the Dell monitor was given a 59HZ refresh rate. There were two choices under the HD graphics setting, one being 59Hz the other 60Hz, so might be worth checking as 60Hz.
I do have something similar. I'm using Windows 7 Ultimate x64, Gigabyte GA-MA-Z77M-D3H motherboard, i7-3770K CPU, Hewlett Packard ZR24w (DVI) and Samsung 2493hm (HDMI) monitors. Everything seems fine, but when I start Civilization IV game both monitors begin to flicker from time to time (approx. every 1 minute). I did not play other games, so I can't say wether there is such issues in them.
Is there any other display you could use to verify the issue is not specific to the Scepter Display? Also, what graphics driver version did you see the issue on?