Actual system ID not found on target at base address

First of all load your fpga design with jtag; at this stage don't use flash programmer, nor try to load it into epcs.

Then, make sure the expected configuration is working; as I suggested, I usually implement a free running counter with a LED connected to the MSB, but you can use any other method.

At this point you should read sys ID and timestamp with Eclipse tools. If they can't be found, then you probably have a flaw in your design: it could possibly be a problem with reset signal (unconnected or wrong polarity) or a missing clock.