Cyclone III Configuration Problem

I thought the same thing but I validated that the pull-up is measuring 10K Ohms. I checked that it is at least connected to +3.3V and the VIA thats connected to the ball pad (this is a BGA package). The only thing I do not know is whether the trace between the pad and the VIA is broken, however, I think this is unlikely. I checked that their is a good trace on a raw PCB so if it were broken it would have had to happen to all 50 boards during the assembly process. One thought that I had was that maybe the I/O bank of the FPGA that the CONF_DONE pin is under never powered up. The CONF_DONE pin is part of Bank 6 and the nSTATUS pin is part of Bank 1. This might explain why part of the chip seems to be working and not the other. If this is the case then my problem could simply be that the Assembly house failed to properly solder the FPGA to the board both times. This also seems unlikely as they have successfully built this board for us a couple times in the past.