Have you tried different keyboard model?
This may be an issue with USB ports, when you try different devices such USB flash drive or different keyboard you will test the USB ports on the computer.
If you still have same problem after testing the ports, you may need to contact Intel support at 916.377.7000 or through their chat service at www.intel.com/chat
I also did a new build today with the same model (D54250WYK) and all was going great with Windows 7 clean install.
...until I installed the latest Intel USB 3.0 drivers from the website. Upon boot now (I had booted several times prior), the wireless keyboard and mouse that was working no longer is. Wired keyboard/mouse does not work either.
It does work to allow me into BIOS where I have confirmed all USB ports are active, etc. So basically, no USB connectivity after the USB driver install.
Ideas would be appreciated. Thanks