Btw, someone happens to need this in year 2022 ( 😃 )and using ISE 14.x (as I don't think Spartan-3 is supported by anything after this, i.e not in Vivado ..) ,
using recent Linux kernel I found that I had to restrict the Digilent HS1 Jtag cable to a USB2 port, while if used on USB3 the libftd2 , as comes with old digilet adept stuff for the board, would cause kernel errors/bugs & oopsies. haven't tried upgrading to latest libftd2 at the date, as this may cause perhaps other issues for the older apps, but at least now I can program that FPGA from the ISE's IMPACT, and the Digilent's command line utility above.