We are also facing the same problem, but only with some of the target boards. The boards are same in all respects and we are using Parallel port JTAG as well as USB-TAP.
The problem is on some boards, the code gets downloaded instantly without any problems, but on some boards I am getting "Unknown Protocol Error"...
As you pointed out in solution, the cable is the same for all the boards, still this issue is there...
Is there a possibility that the processor chip may be faulty??