Cyclone IV nCONFIG pin is not stable

I agree that the worse stuff than a non-working board are those "magical self-healing" ones. These tend to fail operation later and that is annoying. Nevertheless I'd suggest to work on with your code and check the schematic and layout once again prior production of new boards. You should also check the pinout of the FPGA in the schematic to match the pinout file from ALTERA. Just as a sidenote - if you used the symbols provided by ALTERA you might find it worth checking these as well as these are generated by humans as well and while it is very unlikely these can also include a mismatch.