Same problem here, epcs flash programming with 9.0 produces a bootable board, but with 9.1 the board won't boot.
Turning off "generate compressed bitstream" option didn't work for me. I'm using Cyclone II.
The SOF file itseld seems to be working fine, since programming it directly to FPGA makes it operating correctly.
I've noticed that using sof2flash routine from 9.1 produces different flash-file than sof2flash from 9.0 using the same SOF file as input for both.
The difference is within the first 64 bytes of the .flash file, so that's probably the cause of non-bootable EPCS.
I've reported this to Altera but haven't got a solution or confirm about this bug yet.
Regards,
Jari