Due to a problem in Quartus® II software version 9.1sp1 and later, Fast Passive Parallel (FPP) configuration using an Enhanced Configuration Device (EPC) may fail and CONF_DONE may not assert.
To work around this issue, use the Convert Programming File utility with Post-chain bitstream pad bytes option to convert a SRAM Object File (.sof) to a Programmer Object File (.pof) for the EPC device.
Click Advanced... in the Convert Programming File utility and enter 2 or 4 into Post-chain bitstream pad bytes field when you generate a .pof for FPP with EPC device.