ChipScope Pro Analyzer is not able to connect and to initialize the JTAG chain when using a Spartan-3 50. It works fine with any other Spartan-3.
The IDCODE for the Spartan-3 50 is wrong in the "device.lst" file (0140C093=XC3S50 instead of 0140D093=XC3S50).
To work around the issue, edit the "device.lst" file, in the ChipScope/data folder.
Replace the line 0140C093=XC3S50 by 0140D093=XC3S50 (line 3).
This will be fixed in the ChipScope Pro 6.3i Service Pack 3.