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In Quartus GUI, go to Assignments>Device>Device and Pin Options and deselect the option "Generate compressed bitstreams". (This is for Linux web version; Windows version may have this option in a different menu.)
Or throw away the .pof file and use the command line to convert the .sof into one that works:
quartus_cpf -c -d EPCS16 project.sof project.pof
Both of these worked for me (I have a DE2-70 board and had the same problem with active serial programming on Quartus 9.1SP2).
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Neither compressed or uncompressed worked.
I can program the EPCS if I use a JIC file. The trouble is that I need to also program the NIOS elf file. The JIC overwrites the elf and using the flash programmer to put them both, the sof file won't boot. If I could use a pof or a JIC with the elf, then I would be set.
The other thing is this is not a generation problem. I had generated the same file with two sets of files, one under SP1, the other under SP2. Neither would work when I used the flash programmer under SP2. Both worked when I went back to SP1. The problem is not the generation, but is probably in the bootloader that is placed in the EPCS device at the beginning.
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