Remote update EPCS file format?

Thanks for the quick reply. The bits are reversed. The EPCS is programmed correctly, which I verified by reading the contents of it using the Examine feature of the Quartus-II programming tool.

The only difference in the data programmed into the EPCS between the working application config and the non-working application config is the first handful of bytes in the .rbf file. I used the same .rbf data (except for those first handful of bytes), the same programming function in my Cyclone part, the same factory config, etc.

So what would cause the .rbf file generation to produce a file with only a few bytes different from what it should be? I suspect I might have some option in the file conversion tool set improperly, but I'll be darned if I can figure out what.