Hey Mark, impressive lap times indeed. I was actually at Laguna that day as well--in the green run group. My best was a 1:47.9, tho it was only my third day driving that track. Hopefully I'll join you down in the 44's before too long
In terms of this thread, I think that bigjae may be on the right path. If you were to have dyno'd the engine with the bolt-on SC, you likely would have found that you are actually not getting much additional power in a track setting (compared to, for example, street driving situation, which is a lot different). The data you provided actually confirms this. If you were getting, say, net 100hp more with the supercharger at the track, your speed down the two straights would be higher--a lot higher. That's just simple math. But it isn't. (I agree that track surface conditions and ambient temperature/humidity may play a role, but it would be small and thus inconsequential.)
I know nothing about the particular supercharger you used, or what other mods were done to accomodate the supercharger. But I think the conclusion here is that the supercharger, as installed, wasn't designed/setup for track use. Sounds like the basic issue is heat. Running with it on your car at a track when it is not performing optimally could slow you down. It is adding a 40lb lump at pretty bad location (up high, and in front of the front wheels), it will drag on the engine just like running the A/C, and it could affect the stock throttle responsiveness (which is one of the great attributes of the car), & etc. That may actually explain why your lowest low speed is actually with the supercharger on the car.
So I guess I don't find the results to be all that shocking--I'd sort of expect it.