The FT256 package shows the pins in the top left corner of the die in the incorrect locations. C1 and C2 are shown on the top side in Floorplanner and on the left in Floorplan Editor, PACE, and PlanAhead.
This problem has been fixed in the latest 10.1 Service Pack available at:
http://www.xilinx.com/support/download/index.htm
The first service pack containing the fix is 10.1 Service Pack 1.