I have the same problem with my 749R and to be honest i really thought that something was loose on the front end and it made me feel very wary the first once or twice that it happened. The bike seems to get this vague wandering feeling in the front as though there is a strong sidewind and had me really concerned as my 999S did not do this. I have not touched my suspension settings ,I just presumed that they were correct from the factory. It is going for its first service soon ( overdue, dealer busy) so will mention it to them.
My 749R is totally stable right up to 150 mph (obviously on closed roads officer ) , suspension is set as per MCN guide for 999S , I weigh 11 stone + leathers...........................
I had a similar problem on my 999 at brands hatch going down pilgrims drop earlier this year it was particulaly bad when overtaking at speed, Last week under the same circumstances the bike was totally stable. the diffrerence?aftermarket race bodywork with no conformal aerofoils at the side and no upper air ducts in the nose cone. Try taping up the top air ducts (not the air box inlets) and see if this improves things, most 999 riders who noticed tjhought that the bodywork was far nicer looking than the standard stuff