I've instantiated the design fromSOPC builder for the Cyclone II board. As far as I can see I've implemented exactly the same banks and everything else as in the example design. Apologies, I missed that the top message was using the standard example design, I'm using the same board but a new project.
By removing the offending commands I was able to synthesis the design, so it doesn't really matter any more. But I assume that these instructions are included for a reason? I would like to not have to hack these out of the assignment file if I could.