VIP Control is Mutilating my Image!!!

I didn't realise it but there is another control packet, not long after the 1st one, coming out of the scaler. The second one contains the a correct control packet with width and height that I can control through the Nios2. See attached image.

Could this be because the scaler can't keep up with the input? My cvi fifo is currently 1280px, or one line. This is sensible as there are about 400 px of sync/blanking period in which no pixels are clocked in, and in this time the fifo should drain down - perhaps not enough? I've got the scaler running off the pixel clock at the moment, I'm going to compile a design now where the video path is clocked 10% faster than the pixel clock, from a different base clock.