I too am confused. I compiled the system about 5 or 6 times today to try different combinations; if I leave the two pins with their old assignments, everything works fine, if I reassign the two (only using MOSI and SCLK) to the previous location I was using for the individual pio lines (i.e. 2 bits), the debugger would not download and threw the message I indicated earlier. If I leave the two PIO lines blank in the pin definition, it works...
I am beginning to think it may be some sort of incompatibility/bug within the Cyclone II or the SPI core. If I reposition the location of the SPI within the SOPC builder, would this change the location within the FPGA? I am just trying to think of some work around to resolve this impasse. Any ideas are welcome!! Thanks.