Bit confusing. You close the choke for starting, fully open is when the engine is warmed up and will idle with no choke.
The choke knob/lever closes choke plates just before the throttle slides, causing high vacuum at the throat and sucking a lot of fuel into the engine... a cold engine doesn't vaporize fuel very well and this makes for a mixture rich enough to fire. Some (ie your) carb banks have a cam mechanism to increase throttle when the choke is applied... that means you don't have to stand and work the throttle to keep it from stalling. Once the cylinders warm up a bit the fuel spray is vaporized fully and it doesn't need the added fuel from a choke.
Probably the choke idle cam is now misadjusted. There's an adjustment in there, not sure how it works on your bike. But this problem suggests that the slide adjustments were done wrong in a carb sync attempt: it is way easy to do that so the choke cam is off... whereas changing the choke cam setting is not a common adjustment. This can cause trouble with the throttle, either it is unable to open the slides fully or the idle adjustment doesn't work properly (or both).
Anyway, there is a spec for the choke idle cam setting in the service manual, usually a gap between cam and actuator with choke open (off). The RPM should be maybe 3-4000 with choke almost fully closed (the engine will probably choke out and die with it 100% fully closed when warm).