Yes, the external master clock (EMCCLK) is also used during the time from JTAG, when the Flash memory is being programmed. The EMCCLK is used to clock the Flash memory controller, which in turn clocks the Flash memory itself.
Because I have a working bit file and is able to program FPGA via JTAG and the Done LED is ON. But when the FPGA boot from Flash (mcs) it doesn't program and the result is the Done LED is off. I was wondering maybe the eexternal osc is bad.