I had this problem, but sorta solved it (fingers crossed) so I'll let the mods move this if they want since it appears not to be a problem...but thought I'd post here in the event it helps others having similar issues.

I have had some intermittent issues with the bike not wanting to stay running at the set idle speed when I slowed from a decent cruising speed to stop at a light/stop sign, etc. When I did come to a stop, the idle (usually set about 1600 RPM) would drop considerably and in some instances after slowing down from higher speeds (around 55-60MPH) and using a little engine braking and NOT slamming the throttle shut, the bike would actually choke out and die. And at regular idle, the longer it idled the lower the idle seemed to get, sometimes staying running and sometimes dying. Note that I know all about the air/mix and mine is about 3/4 out and is not part of this problem

I also have noticed some soot on my rear brake adjuster giving me a clue that something was rich. The questions was WHERE was it rich.

I did some educating in our help documents, and more importantly at this site (because it has a REALLY good overview of the carb workings), which is where I think my light bulb went off:
http://totalruckus.com/phpBB3/viewtopic.php?f=28&t=82639

What I surmised is that when I raised my needle last year to fix a slight shutter around 1/8 - 1/4 throttle, I went too far. When a bike stops running we want to always think that it NEEDS MORE GAS, which isn't always the case.  In my case, what was happening was as I slowed from a higher speed that meant MORE time for the bike to be idling and a bit more time for (in my limited knowledge) the long engine braking to maybe hold the plunger open ever so slightly in the 1/8 range where the needle has an effect. That combined with my needle being set too high meant that excess fuel was building up and FLOODING the bike. After each time it would die on me, I would have to try starting it 2-3 times before it would crank up and run, and when it did I could see the 'puff' of soot blowing out.  This would also happen when idling and I hit the throttle hard...It would hesitate a second and then rev up and give little puff's of lightly visible soot.

So, I have a Dynojet needle with adjustable clip and I moved it back up to the 3rd notch (pushing the needle down) but also shaved a bit more off of my white spacer (raising the needle back up) for a net needle lowering of about 0.75mm.  

Problem solved. Bike is running near perfect, no noticeable hesitation at 1/8 - 1/4 throttle and when I come to a stop the bike returns to idle near perfect with no dipping down below my set RPM or acting as if it is flooding or trying to choke out. Remember, a symptom of RICH is idle dropping (because of flooding) and an idle hanging at higher RPMs for several seconds or so is a symptom of LEAN. I know, sounds backwards but once you understand the physics it makes sense.

So...if you have issues with stalling at stoplights and you have visible sooty residue and you have adjusted your "white spacer" or needle considerably thus raising the needle, take this into account and ask if it may be your issue.

If this didn't work my next step was to try a smaller pilot jet, but based on my symptoms (issues all at idle to 1/8 throttle position) and noted results I think (knock on wood) that this little tweak is all it needed.

Ok, now fire away and tell me how wrong I am?!?!    Doesn't hurt my feelings because, right or wrong, it worked for me  

Glad you got it solved.  I notice on my bike when I raised the needle too far it made a weird sound as I rolled off the throttle and begin to decelerate....the engine made a kind of a growling sound that wasn't there before and it was a bit sluggish when you rolled the throttle back on.

Carbs can be mystifying sometimes.  I have been fighting a situation on my Ninja this year that wasn't there last year.  I may have found the problem last night as I took the carbs completely apart and cleaned them.  It appears I oiled the new foam filter too much, and the slides got coated with the sticky air filter oil and they were hanging up when they needed to make minor movements - for some reason they didn't hang up until the engine warmed up a bit....and some days they didn't hang up at all - other days they hung up a lot.