--- Quote Start ---
Any other pins shorted or not connected? I had such problem, when one wire was not conntected to the JTAG connector properly.
--- Quote End ---
I just rechecked all the connection pins. None of the JTAG pins are short nor, are they unconnected. The board is using a FT2232 USB-JTAG converter instead of USB blaster-MAX CPLD as in normal dev boards from Altera. The converter(FT2232) seems to be working, but the FPGA doesnt seem to toggle the TDO pin, when detect command is thrown, thats why the warning "TDO stuck at 1"(correct me, if i m wrong). How can i check that the FPGA is faulty or not ? Since this is a custom made board, they havent connected any LEDs for indication that it has passed the chain test. Forgive my ignorance, since i m doing board testing for the very first time.
Regards
Jeebu