This happened to me once years ago before engine management systems. Cause was lots of high revs and high speed runs with a weak mixture caused by me altering the airfilter to a more free flowing foam type.
Has the head been skimmed and the valve clearences not adjusted to compensate?
Is it possible for this engine, with its management system, to run weak and hot due to your induction changes?
The only other recent case of valve burn I know of concerned a bloke who constantly ran it against the limiter as though it were a computer game.
Hope you get it sorted
Regards