DE0 Nano problems getting pins to work

I am working on a design with a De0 nano board, and I am having problems with getting pins to work. Quite a number of pins are working OK, but others dont output. In particular, pins A12, T13, R13, T12, do not work. I have rerouted the internal signals to other pins and they work, for instance the signal to A12 was rerouted to C9, and then works fine.

So, a couple of questions.

1/ Are all the pins on the 40 pin expansion headers dedicated to the headers, or do they have other functions?

2/ I presume all pin assignments as shown in the latest version of the user guide are correct?

3/ Is there some other way of setting up pins apart from the pin planner? Everything in there seems to be correct.

I am also having problems with Quartus, including the verbal garbage that the reports spew out. I put in two pins and although they were in the .BDF drawing, and I could partly assign pins in the pin planner, and the pin names would appear in the .BDF drawing, on compilation the compiler would not recognise these pins and gave a message that the nodes were not in the .BDF drawing!! I hand edited the .V file that the compiler generates, and got the pins to appear.

All very frustrating!

Any help gratefully received.