I recently tried out Petalinux on the exact same board, with the same tutorial (I was using the hardware reference design for the RevD board though, not RevC as specified in the tutorial). I remember having some problems with missing files due to me using a split Windows/Linux development platform (Windows for Xilinx tools, and Linux for the rest) – but it sounds as if you're using Linux for everything?
Regards,
Simon Falsig