Using JTAG after the system is booted is common during development. However, when you do this the endpoint might link train properly, but it is not enumerated or configured by the system, so it is not recognized at this point. Issue a warm restart and the endpointis recognized; see
(Xilinx Answer 34806) for tools that show if the device has been recognized by the system).
See
(Xilinx Answer 37406) for a possible workaround to this problem if using Linux.
Revision History
10/08/2010 - Added reference to 37406.
08/13/2010 - Initial Release