Did you enable any of Fast Boot optimizations in MB BIOS? Also, the reason may be that your 660 Ti`s have a new UEFI-compatible VBIOS (GOP), and DX79 boards do not fully support it, so there are a delay before system find a legacy VGA BIOS.
I have got the same problem!
My DX79SR motherboard does not work with Gigabyte Geforce 780GTX.
During POST, it shows blank screen and 0_ at bottom right corner.
Also similar to the problem posted here. The GF780 is a brand new card, and works on my friend's motherboard, and his motherboard was quite old.
The new BIOS version 0590 is now available under the following link. https://downloadcenter.intel.com/Detail_Desc.aspx?agr=Y&DwnldID=23015&lang=eng&OSVersion=%0A%09%09%09%09%09%09%09%09%0A%09%09%09%09%09%09%09&DownloadType=BIOS
This link belongs to the DX79SI motherboard; however it is valid for the boards below.
Intel® Desktop Board DX79SI
Intel® Desktop Board DX79SR
Intel® Desktop Board DX79TO
• Fixed issue where PCIe Slot 2 does not work with certain PCIe x1 add-in cards.
• Fixed issue with Wake-on-LAN in Linux*.
• Fixed issue where certain add-in graphics cards are not properly detected.
• Updated processor support.
• Improved compatibility with the latest graphics cards.