Lovely looking machine! I had an S2R 1000 too with the same Arrow system and an open airbox. It ran with a Power Commander and custom map and never gave less then 50 m.p.g. so something must be amiss.
Does it smell rich? Do you have the dyno chart from when it was reflashed? If so, it should show the air/fuel ratio (AFR). You'd expect it to be between 12 - 14/1 but I'm sure the dyno tuner wouldn't have signed it off if the ratio was way off. It might be worth putting it back on a dyno to check what the current AFR is.
You say you've cleaned the air filter, so it can't be that.
Have a look a this post from MrsC_772 about a similar problem she had with her 696.
http://www.ukmonster.co.uk/monster/s...4&postcount=23
It turned out to be a leak in one of the sensor hoses. I don't know how similar the plumbing is between the S2R and 696, but perhaps that could be your problem too.
Good luck in sorting it out and keep us informed.