We are trying to program the XS board with a bit file produced with the Xilinx software. I tried a file produced here at UNH and also the one with the download software. I notice that the /INIT pin goes low during programming and stays low unless the board is powered down. I think this indicates an error. I am using parallel port 1. Does you software check for a correctly program device?
When the INIT line is driven low and stays that way, that indicates some sort of programming error. The parallel port interface of the XS board doesn't carry the /INIT signal back to the PC, so there is no way for it to know a problem has occurred.
The most likely cause for this is using a .BIT file for the wrong FPGA device. Make sure you generated a bit file for the FPGA in the socket of your board (such as the XC2S50TQ144 on the XSA-50 Board).
Another source of error may be a problem on the parallel port. Try to download the .BIT file from another PC.