Thanks Dave. I keep trying with the method A but to no success. I followed the DE4 Getting started manual, but the tools are giving a problem. Could you please look into it if you have the time and suggest a possible direction. I understand the catch of configuration time vs the BIOS start time, but am willing to try it.
The weirdest thing with method A is the fpga undergoes a hard reset when , it is programmed with a PCIe system and PC is rebooted, thus losing its configuration. This does not happen when a non PCIe system is programmed on the fpga.