OK, would you explain the thermodynamics a bit more completely than a single word? All I have so far is my own conjecture. Not inter-cooled, so at high ambient temperatures, the blower outlet temps are very high, the engine intake passages get hot which further heats the inlet flow so that velocities get very high and this increases pressure losses which in turn increase the back pressure on the blower resulting in less airflow? Am I getting close? If so, are there data? Does this happen at 59 F or only on hot days?
Since kfennell's response was "heat", I think it's safe to assume your post was addressed to him. He's offline, so perhaps you haven't seen my response, which explains "heat" and other factors a bit better (below).
The factory supercharger (MP45) is very small, isn't intercooled and heat soaks quickly. The extra weight just adds insult to injury.
This is a very general explanation from a forced induction novice.
Whenever you compress gas (air/fuel) with a forced induction device (SC, turbo), heat is produced from the compression. An intercooler is to cool the compressed gas after the forced induction device (SC, turbo), before it enters the cyclinder. Cool, dense gas (air/fuel) makes more power and lessens the chance of pre-ignition/knock, and allows for more agressive timing.
The sizing of the forced induction device is important as it can be too big (lots of lag and a small rpm range of effectiveness), or too small (little lag but doesn't pull hard throughout the RPM range). The size also effects the efficiency. A small device out of its efficiency range and blowing hot air (more heat in the air than needs to be for a properly sized device) in a non-intercooled system can potentially be less powerful than without the SC/turbo, as the cool, dense air/fuel charge we seek isn't there.
Another scenario is that when the entire system (engine, forced induction device, intercooler (or not) etc.) is "cold", the SC/turbo adds power to the system as intended. Once warmed up, or when portions of the system are heat-soaked (easily done with a SC/turbo without an intercooler), cooling the systems (and more importantly the air/fuel charge) won't happen, or takes an extended period of time depending on the IATs etc.
The bottom line is most systems have adequately sized forced induction devices and properly sized intercoolers to add power and sufficiently cool the air/fuel before entering the cylinder, to consistenly produce a baseline of power. The MP45 is just too small to efficiently add power to the system without heat-soaking, and without an intercooler, the system pulls timing and thus reduces HP.
There's a reason there are no aftermarket tunes for the MP45. The system doesn't have any headroom to allow for more power. It's already heat-soaked under normal use.
Removing the MP45 and adding a proper SC and intercooler provides an opportunity for a healthy amount of power.