Just a quick update: Running examine to get what's inside the FPGA and using WinMerge to compare the content of the files (not the best tool because of binary content... anyway), it shows that the content is vastly the same except for a slight difference at roughly a third of the file, where some data seem to be missing in the file read back from the FPGA (difficult to tell precisely, because WinMerge does not show the offset from the beginning where the difference occurs). Anyway, this seems to confirm that something has effectively been programmed in the FPGA, but maybe not at the right location...
jylo