was it a clean install of windows &/or gpu(s)? nvidia drivers installed ok? which version?
have you checked mobo manufacturer website for updated mobo drivers?
Yes, it was a full system build so every component and the OS (Windows 7 Home Premium, although the issue only exists before the OS loads) was a clean install. The Nvidia drivers are 280.26, the latest non-beta version.
According to the Gigabyte Download Center Tool, all of the moatherbord drivers and the BIOS are up to date.
You can just get over it and use the DVI regularly, no difference between HDMI and DVI... only the Sound output from the HDMI and the cable width
But if you want to troubleshoot the problem you can try to set the Monitor Input to be HDMI, also it might be that the HDMI from the GTX 560Ti takes a bit long on detection.