With ChipScope 6.2i, a known issue causes the reprogramming of a Spartan-3 to fail. Sometimes, the programming will succeed, but the design does not work correctly.
To work around this problem, try using iMPACT 6.2i to program the FPGA:
1. Run iMPACT to program the FPGA.
2. Exit iMPACT.
3. Run ChipScope Analyzer.