There is a bug in SAM 2011.11.24 that prevents the "Calculate and plot" button from working correctly when you choose the "amorphous" cell type. We will fix this problem in the January update.
However, if you choose the "amorphous" cell type and run a simulation (without clicking "Calculate and plot", the simulations should run without errors or notices. The simulation notice you see is because you ran the simulation with the "multiSi" cell type.
Best regards,
Paul.