Hi, I have a 2003 XT600E and it does the same thing, has always done it since new. New air filter or not.
The exact rpm at which this occurs depends on the gear, but 2,900 in third
3,200 in fourth etc.
Like Bernard, I had assumed that this was where the second carb was cutting in and that it was "fluffing" just at this point. Anyhow, it makes the bike like a bad tempered mule to ride at these speeds (gearbox comments noted) but 3000 rpm and third gear = 30 mph. So, around town this is a desirable place to be, second gear @ 30 mph is to much.
Don't they all do this ?