https://en.bitcoin.it/wiki/CM1Quickstart, but remember about hashvoodoo spartan-3 controller firmware.
I've got that problems with CM1 too in IMPACT&Xilinx JTAG and don't know why? Too long JTAG chain or bad PCB design?? Who knows that?
I use a cheap Xilinx USB Cable (DLC9G clone) to program all my boards the only trick is setting the dip switches 8, 6, 3 to off and plugging the program cable into the controller JTAG which is above SW6 and using Xilinx ISE (14.5, 14.6, 14.7) start Impact and it will detect the chain and program successful unless you did not set dip switches!
I never got the official way working consistently hence my use of the program cable and Impact, works every time for me on multiple boards