Mine (2002 single spark - 17000 miles) has been doing this for the last few thou miles.
Even a super accurate valve adjust and throttle body balance (around 5000 under load with twinmax on tank) hasn't completely cured it. I have even been around the bike tightening things up in an attempt to sort it.
Problem is when you have ridden it like this for a bit, you forget how smooth it has been - but Im sure it used to be a lot smoother than this through 5000.
If you find an answer, let me know....