Cyclone III configuration problem with Active Parallel flash

Ok, I got it after talking to Altera support.

It seems I needed to follow the instructions written in "NIOSII Evaluation user guide, Cyclone III edition":

http://www.altera.com/literature/ug/niosii_eval_user_guide.pdf

Once I did the steps stated in page 69 and forward, I managed to place the configuration

and application data both in the flash memory, and boot from the flash.

Still, this is a mystery. There's hardly any explanations as to why those steps work.

Altera should take note- the documentation on this feature is not good enough.

Does anyone know of an app note or such that explains the boot process of the cyclone 3, the flash contents, etc?

Ran