In Cyclone® III and Cyclone IV devices, when writing a parameter such as the application image boot address, watchdog enable or watchdog timer value in the factory image, the read_source[1..0] has to be set to 00.
Even though this read_source port enables you to select the read source from the current status or previous status when reading the status register, when writing in the factory image, you need to set 00 to select the current status which is the factory image mode.