Pin assignment problem---FlashRom Open Drain

The same error has been reported in another thread, I think. However, I don't understand where the Open Drain setting comes from, it seems inappropriate for any possible usage of the flash pins. I'm not using the board nor Cyclone III with AP configuration, so I had no occasion to experience the problem. But I know that the starter board is shipped with a fully operational example project, cycloneiii_3c25_start_niosii_standard that also uses the flash. So I first would compare with the pin configuration used in this project to understand what's wrong with your configuration.