I realized that problem had occured due to loading incorrect binary file into eeprom. Since at start-up, cy boots from eeprom, it was failing to start properly.
In order to solve the problem, I shorted the two pins of cy, that is GPIO_30 and GPIO_31. These pins are also connected to the 24LC128(eeprom) as given in the schematics of ML403 board. I turn on the board with that shorted pins, then computer recognized the cy. Then, I disconnected the shorted pins, afterwards loaded "eeprom.bin" file using qtui2c command. This file is provided in the xilinx web site for USB reference designs of ML40x boards. ( http://www.xilinx.com/products/boards/ml403/reference_designs.htm ). Now cy works properly.