'error loading design' when simulating sopc system

I'm having trouble simulating my SOPC system in modelsim. I click 'run simulator' and modelsim starts. I then use the s macro but get 'error loading design'.

The compile report summary seems to indicate that some include files aren't opening

Error: C:/Altera/91sp1/quartus/de0b/steveprosopc.v(14766): Cannot open `include file "altpll_0.v".

** Error: C:/Altera/91sp1/quartus/de0b/steveprosopc.v(14767): Cannot open `include file "AVALON_FFT_WRAPPER.v". etc etc.

I have the FFT IP within my system. Not sure if i'm doing it correctly, or if this could originate from errors in my code - but everything compiles ok and my software runs as expected in nios.