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The ECU no doubt will have ignition and/or fuel correction maps based upon intake temperature - the higher the temperature, the more advance that is taken away and/or the richer the car runs. This is why it's best to to comparative dynos around the same temperature if you can, so you are comparing apples with apples. Sure SAE correction accommodates air temp, humidity and pressure changes but if the car is subtracting a couple of degrees of ignition timing, you will obviously lose power.
The other thing is to try and get your coolant temps and oil temps the same for before and after runs, as there likely will also be ignition correction maps based upon theses temperatures.
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