Pete,
I'm retaining some skepticism myself as this is only one piece of evidence from one rider. However, as far as I know this is the first time anyone has done an experiment of this type.
To address your questions:
1) The original certified cal course is actually 1309.98 feet. I remeasured it a couple weeks ago in order to run this experiment and lengthened it to 400 meters. I have discovered recently that when I thought I was applying 10lbf I was actually pulling a good bit more, so in all my cal course measurements, including this one, I now use a little clamp I attach to the tape and a fish scale I hook onto that to make sure the force is 10lb. When I remeasured it I put P-K nails at every hundred meters along with small white spray paint lines. When I saw the results of the experiment I became concerned, so I went out this morning when it was about 68 degrees and measured it again. On this measurement I found the hilly 200m to be 200.005m and the flat 200m to be 199.995m.
2) I tried to keep my riding posture the same on the hilly course and the flat course, but there is some unavoidable shift of weight on the different rides. I think that's what we're measuring here though.
3) The riding surface on the two courses is different. The flat course is entirely recently-resurfaced asphalt while the hilly course is almost entirely concrete. Both are in good shape with no potholes and few cracks. It's certainly possible that this is causing some of the difference I'm seeing, but if the change between asphalt and concrete is the reason for all the difference, that would be its own cause for concern.
I should mention that I used randomly placed pieces of tape as the end/start points of my rides, so I had no idea what the numbers meant as I was taking measurements. This is described in my post about the length experiment I did. Also, I used a marked-up wheel to record wheel revolutions rather than Jones counts.
I would love for someone to repeat this experiment, but it might be difficult to find the right spot. Finding a 200m section of flat road right next to a hill is not as easy as you might think. Google Earth is a great way to look for such a location, however. I was lucky that I had something pretty close to what I needed right in front of my house.