When I wrote my first reply, I based my answer understanding that the OP experienced an exhaust flap stuck in open position, and this made an impact on the startup of a cold engine. Then, after a few seconds, the engine reverted to act more like 'normal'.
And after fixing the the flap, stuck in open position, the problem disappeared. I also interpreted this as the flap, when being fixed, reverted to remain closed when engine was started.
My information about the 'ways' of the newest Bosch ECU's was something I stumbled across as I searched for information about how Bosch handled the WB O2 sensors (New in our bikes, but it has been around for a few years in the car world.)
There was a chapter debating the effect of restricting evacuation of the exhaust, containing unburned fuel, especially before the engine warmed up. The EGR valve is the main tool for this in cars, but they also where working on expanding the use of the exhaust flap from being merely a noise restricting tool to a means of restricting the exhaust from all of the exhaust to escape the cylinder, as well as a potential blow back. The blow back may be looked upon a bit of the same effect you get if you try to fill an empty bottle of water and then open up the tap to a full blow.
Anyway, whatever the flap does to the newer engines, keep in mind that for the first few seconds, the fueling is 100% relying on the preprogrammed mapping. The heating of the O2 sensor starts when the engine has started, not sooner, and the warm-up time is typically 10 - 15 seconds.
Now... If the engine is set up for a more than average exhaust remaining in the cylinder, motivated by less pollution and less filling up the cat by unburned gases (which is very damaging for the cat), the only means of doing this for a short periode of time is by using the flap, as, even if the flap allows some exhaust to by pass, the pipes will still be flooded by exhaust above average, a bit like trying to get off a train when the apron is congested by people blocking the exit. In this scenario, an open flap would allow for less remaining exhaust in the cylinder, thus allowing for more oxygen entering the cylinder.
If this theory is real (and also, keep in mind that Bosch has claimed to be working on this,) the fueling at this stage is preprogrammed for less oxygen entering the cylinder, hence adding less fuel, and no feedback from the O2 sensor, as it's still warming up. The engine would be running rough and would be needing more fuel, hence opening up the throttle. Opening the throttle means opening of the flap, allowing for a preprogrammed sceniario where the flap would open anyway, which means a pre-program to add fuel based on a higher percentage of oxygen entering the cylinder.
And then, after the O2 sensor is warmed up, the fueling would be adjusted based on feedback from the exhaust, and the throttle may be released, allowing for a smooth running engine at idle even with the flap stuck in open position as the feedback from O2 sensor now would compensate the fueling.
If after testing, hopefully sometimes this weekend, shows that the flap is open also when starting and running a cold engine, this theory will be shot, and we may conclude that the whole experience by the OP was merely a coincident.
Time will show...
PS.
I would also like to add that I do appreciate this debate, where everyone is debating and challenging the technical part of what's happening rather than clogging the debate with nonsense