The little "spits" or "sneezes" through the carbs is usually a condition of the mixture being too lean. Do you have the mixture screw plugs drilled out? You could open up the mixture screws a bit then adjust the idle to where it should be.
The only theory I can come up with regarding why this is happening now after a valve adjustment is that you said all were too tight except an exhaust valve. If the valves are too tight they don't lift as much and only suck in enough fuel/air mixture as the tight valves will allow, robbing you of power because of the less volume of fuel/air mixture in the cylinders. When you open up the valves to their proper spec the engine will try and suck more fuel/air mixture into the cylinders on the intake stroke than when the valves are tight. If the jetting was borderline lean, like all Bandit 1200's stock jetting is, than it might not get enough fuel/air mixture to consistantly have enough fuel to air mixture ratio to consistantly detonate on the power stoke. Hence richening up the mixture a tad may compensate. They really shouldn't be affected much though, weird. Anyone else have a theory?
BTW the bike should idle at 1200-1300 when fully warm. If you run it any lower there is not enough top end oilflow at idle.