I believe you can examine the contents of EPCS; you may have to play around a bit. The idea is to do an "examine" and then File --> Save as (although I'm probably not 100% correct on this -- I'd imagine there is some Quartus literature that explains it).
One other thing that comes to mind (but not explained by the similar sizes you report): In the quartus covnert programming files tool you can optionally turn on/off FPGA bitstream compression when creating your JIC file. I believe you have to select the FPGA-configuration and then hit the properties button to display this dialog. This would indeed change the configuration data significantly.