The ecu does "refresh" itself when shut off/on , also when it idles for a certain amount of time (i wanna guess 30 seconds) it will refresh itself, you will notice when you start your sled from cold after a certain amount of time the idle changes, usually drops.
You may be able to go up/down a couple thousand ft and your sled still run, as the slight variance in duty cycle is minor compared to all the variation in fuel pump, filters, injectors etc...
This issue was much more amplified in some of the previous turbos I owned as you were piggy backing a % off a %. There was times coming down from high to low elevation, sled would bog , hit the kill switch ,re start, and sled was ripping again.
If you have a any buddies with pros it would take 5 minutes out of your ride to swap TMAPS / EGT Sensors, and would answer your question 100%.
I still think as you said it only happens at the start of the day it is because of a cold pipe, coming down at the end of the day it runs good you said which would eliminate tmap for me.
The engineers would love to drop some extra weight and get that pipe insulation and cover off the pipe, but it is there for a reason. 2 strokes need that pipe hot.
Im going to ceramic coat and wrap my pipe, win/win for performance and under hood heat.