The JTAG driver is being held by another instance of a Xilinx program. When it happens, disconnect the JTAG USB cable, close SDK, and turn off the Perseus.
Make sure all SDK processes are stopped after closing the SDK window. Sometimes, javaw.exe software is still running and must be close manually in the Windows Task Manager dialog box.
Turn on the Perseus, connect the JTAG USB cable, and reopen SDK. FPGA programming should now work.