When I launch Floorplan Editor for Spartan-3, Spartan-3A, Spartan-3AN, and Spartan-3A DSP devices, the Vref pins and right side I/O pins are not displayed in the package view.
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.