They updated this on my toy, delivered 01/10/04, at the 600 service and it seemed to soften the hard take up at low revs.
Having experienced similar roughness with a Ducati 916 I find that after riding the new software for a short time it is difficult to have objective hindsight.
I think your dealer will update on request, though he may try to put it off until the next service, just to ensure you do not save money by diy.
I also found that a sensitive throttle hand, especially on upchanges in the lower gears, really pays off. Hardly any easing of the throttle works best for me. I think this is due to the equally spaced firing order of a big 180 degree twin, the Ducati is less sensitive in this respect with the 90 degree split.