I've had the same experience (or, perhaps more accurately, non-experience) with my '07. We may each be entitled to factory refunds.
Can such a small aerodynamic area as presented by the fender raise the havoc reported? Some say, "Yes," and indeed they might, given the complexity of the aerodynamic profile of the KLR650 at speed and in crosswinds.
In this case, perception is reality; if swapping out/modifying front fenders fixes the problem, it's fixed. Fortunately, the problem has yet to materialize for me; I do not doubt those who actually experience it.