There are no differences between the 2007 and 2008 engines that would account for the speed difference. Its probably something simple like the throttle bodies on one or both engines are not opened all of the way. There is a minor difference in weight due to the rear access hatch and what appears to be a thicker hull section near the water intakes. Also if the 2008 model has less than 7 to 10 hours on it the speed should be slower than a broken in model anyway. The first seven hours of a SCIC engines is deliberately set to have retarded timing and increased fuel flow, both of which will impact top speed. A slight difference in wear ring clearance could also account for a speed difference.
Boat test magazine did a test on both boats. The 07 like mine showed 57.4 mph just like mine on GPS. For the 08 it showed 52.? mph just like the one from our shop. Does not matter now anyway as I have placed my order for the 09 510 hp model which supposedly runs 56.?? but has the newer features and the updated engine.