I think this is part of your problem. A course with starts and stops is not a good choice for isolating the speed difference between the bikes. Your average speed on the course will be determined by the starting and stopping as much as anything else. Looking at the two bikes in your picture I'm not sure there should be a big speed difference if the suspension fork has a low loss lockout function. I'd try to find a test course on a bike trail that has no stops at all and then make several runs on the two bikes alternately on the same day to try to eliminate as many other variables as possible. Obviously your engine will tire during the test process but differences between the two bikes should stand out as a change in speed from one run to the next in spite of the general loss in speed as the engine tires.

Ken