In the Project Navigator GUI under "Generate Programming File Properties", there is an option to set the configuration rate to 100 MHz. According to the "Spartan-3 FPGA DC and Switching Characteristics" data sheet, a 100MHz configuration rate is not a supported configuration frequency as defined by the parameters Fccser and Fccpar.
The Spartan-3 configuration logic does not support a configuration frequency of 100MHz; consequently, the 100MHz option should not be an option in the Project Navigator GUI.