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Judging by your JTAG chain, you seem to be using a cyclone V SoC chip. However, in your Convert Programming File dialog, the BSP_DUAL.sof file seems to be for a 5CSE (Not SoC) chip. This is the mismatch that it is complaining about, not the serial flash. The SoC chip should be either 5CST or 5CSX. Your bitstream file was created for the wrong FPGA. You need to build the sof file for 5CST or 5CSX.
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Nope, the 5CSE is definitely a SoC chip, it just doesn't have the high-speed transceivers that the 5CST or 5CSX parts do.
http://www.alteraforum.com/forum/attachment.php?attachmentid=11681&stc=1 My full part number is the 5CSEBA5U23I7-N, which is a Cyclone V SoC, 85K Luts, UBGA 672 pins, Industrial Temp, with Dual-Core ARM-9 Processor (Lead-free)
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