While the throttle plate not responding correctly or various other problems could cause stalling, most of the time stalling when stopped/idle are fueling issues.
Your ECU learns how much fuel is needed at a given mass of air in order to run at the designed Air/Fuel ratio. It then modifies the injector pulse width by up to + or - 10% to compensate for both mechanical differences and environmental differences.
Every motor and environment is going to be a bit different and require differing amounts of fuel to keep the engine idling smoothly. You can be quite certain that your environment is different from the one the motor was born in. And that your motor will break in differently than someone else's.
The older GS manual said it can take up to 100 miles before it has collected enough data to learn how much it needs to tweak the injector pulses to achieve it's designed A/F ratio at idle.
Until then, it very well could stall or idle rough, or let out funny colored smoke. No mystery.
All three of my Spyders have done this when new. It's annoying, but it's a lot less irritating (or to some people, infuriating) once you understand what's happening and that it's temporary.
If it bugs you, take it to a decent dealer and ask.
how could you have air in fuel system? Maybe in brake line but not in constant flowing fuel system. Or am I missing something that is on a spyder that I have never heard of before. 
hyea:
