I don't know exactly how that auto-choke works... but I would not trust it while it is acting like you describe.
Try to disable it.
Yamaha 2 strokes use Mikuni carbs almost exclusively... Mikuni carbs usually have a choke that is a plunger which goes up and down...
when the plunger is down > no choke
when the plunger is up > choke is on
disconnect the linkage or hose(s) running to the plunger and see to it that the plunger stays down (wire or tape?)... the choke will be off and now you should run it to test it.
this is mostly guesswork on my part... hope it works