This isbecause write_bitstream will not include thecorrect SPI read command if we do not explicitly set SPI_32bit_addr option to either "No" or "Yes."This issue is resolvedin 2012.4.
To work around the issue in2012.3, add the following to project:
(1) set_property BITSTREAM.CONFIG.SPI_32bit_addr No [current_design]
(2) Regenerate the bitstream
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