No it's not the height, it's exactly as you describe. My 2005 R1 does the same. I have replaced both bulbs (from H7 back to stock) looked for shorts and bad connections. I have even hooked up a voltmeter and ridden with the damm thing on the tank with the bulb in and without to see if it's some sort of extreme voltage fluctuation at the socket; which was less than a volt difference from when tested. Also at least on my bike, it wont happen if the bike is in Neutral and parked, I can reb the engine with no noticeable brightness fluctuation; as soon as you put it in gear and drive the problem manifests itself. I am guessing that there is a difference between how the lights get power distributed to them when the bike is in neutral and when it's under load. The only thing I can think of is that maybe that one volt of fluctuation makes the bulb brighter since the lights are magnified it makes a difference.
I am out of ideas, but I would like to get this fixed before I piss off somebody that tries to run me off the road.