I have a Nov 04 12GS which recently had the software upgrade at around 10K miles when in for the other recalls and 'free brake check' (as well as yet another set of new tyres...). I have to say it is smoother than before, especially on small throttle openings, as well as getting rid of what I found to be a very slight flat spot around just under 5K. I have not experienced the surging problem discussed here either before or after the software upgrade: on the contrary, this has been the smoothest boxer engine of the six I have owned. The discrepancy between those who are experiencing this fault and those who are not suggests something is amiss. Maybe a software reload or at least a diagnostic checkover might be worth trying as well as the other mechanical possibilities which have already been suggested. There must be a logical reason why this problem exists in some bikes and not at all in others... 

