I don't have a solution
But, do file a bug report with Nikon. Even if there is a way around this problem, discarding metadata by default is not the right way to go.
Metadata issues are going to be more and more of a deal breaker for imaging applications, and it is especially nasty when one link in the chain discards some of the metadata along the way.
If you're so inclined, take a look at the
Metadata Manifesto from the
Stock Artists Alliance it's a good start on beginning a discussion on metadata related issues and the problems of developing a functional "metadata flow."
Doug