There are some minor discrepancies in I/O net names in SP601 schematics (can accessed from http://www.xilinx.com/sp601)and the Spartan-6 FPGA Packaging and Pinout Specifications (UG385.pdf) and pkg files.
The I/O pin names referred to in the Spartan-6 FPGA Packaging and Pinout Specification and the Pinout Files override the pin names used in the Schematics. The ISE software should be identical to the Pinout Files: