I don't know that I have the right answer. But if you right click on your BSP project and select the "NIOS" menu then "BSP Editor", you should get a window that a bunch of options for your BSP. One of the tabs says "Linker" on it. In that tab, you can control where the BSP tries to put everything you build.
Again, just a wild guess but maybe if you try selecting different memory regions from the drop downs on that page, you might get lucky and make your problem go away. Hope this helps, if it is still not clear I will try to give more detailed instructions when I am back at work tomorrow.