Problem with AP Config on Cyclone IV

I have a prototype batch of boards on my bench I recently designed with a Cyclon IV on it and have it setup for AP mode with a PC28F512P33BFD. I can program the FPGA with JTAG and everything works fine.

However, when I go through and create the POF file, and try to load it to the flash, I'm getting the following error messages, and they don't seem very useful for debugging.

Info (209060): Started Programmer operation at Wed Mar 28 16:28:07 2012

Info (209016): Configuring device index 1

Info (209017): Device 1 contains JTAG ID code 0x020F70DD

Info (209007): Configuration succeeded -- 1 device(s) configured

Error (209025): Can't recognize silicon ID for device 1

Error (209012): Operation failed

Info (209061): Ended Programmer operation at Wed Mar 28 16:28:12 2012

I'm new to using the Cyclone IV, and AP configuration mode, so it might be something stupid I'm doing.

Due to the design of the board (mostly BGA's, tiny traces, and tiny vias) I'm also having a hard time looking at any physical signals to determine what's going on.

Does anyone have any useful tools or tricks to help figure out what is going on?

The only thing I can guess to try would be to set the config pins so I can access them from logic I put on the part with JTAG cable, and try to read and write to the memory part in a simple state machine to get a better idea what is going on.

Has anyone done anything like this with any positive results?

Best regards,

Mike