I would guess air leak or the throttles are not balanced - or not close enough to get the pulsewidths very similar.
Can you get a reading while riding the bike with more airflow going through the carbs?
If you are happy there is no air leak there should be an adjustment to balance the throttles at idle (sorry 950 owner don't know the exact layout of the 990's) you could try adjusting that until the pulsewidths are the same. - also make a note of the idle is smother or not (should be smoother if you are balancing them). The correct way is to balance the air pressure at idle with pressure gauges of course...