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The Quad SPI flash chip isn't on the JTAG chain. You need to follow the instructions for programming a quad SPI chip, not a JTAG based chip. There are some app notes as well as a section in the Altera programmer manual that explain how this works.
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Erm, yes I know the Quad SPI flash chip isn't in the JTAG chain, that's why I said I was programming it
via the FPGA.
When the JIC file is loaded, it is sets the JTAG programmer to load the FPGA with the "Factory Default Enhanced" image, and then the flash chip itself with the JIC image.
When run, it successfully loads the FPGA with the "Factory Default Enhanced" image, the CONF_DONE pin goes high.
Then the JTAG it tries to send the JIC file to the "Altera serial flash loader" core instantiated by that FPGA image, in order for that to be able to program it into the QSPI chip attached to the FPGA. That's when it fails.
AN370 etc are fine, but they do not address the specific problem of how to program the chip I have rather than then Altera's own EPCQ512.
See below image,
http://www.alteraforum.com/forum/attachment.php?attachmentid=11678&stc=1
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