In ChipScope 12.2, the upper quads are available for selection, but the core is not implemented correctly and the reference clock is not connected. This issue is resolved in ChipScope 12.3. An assisted work-around is available in 12.1 and 12.2.
If you require further assistance, open a WebCase with Xilinx Support at:
http://www.xilinx.com/support/clearexpress/websupport.htm