Hello Nick,
a few months ago i got this reference design as well. I got it up and running easily on a EP2C35. My assumption would be that your electrical connection is the source of your problem. Ensure that pixel clock, vsync and hsync are properly shield versus ground or otherwise you will have a distorted image display. I used the proto pins on the EP2C35 board to connect it with a small TFT display using prefab'ed 25cm wires. Without shielding the aforementioned signals i got a distorted display as well. Entangling pixel clock wire with a ground wire did the trick (likewise with vsync and hsync).