I don't really think there's much we can do about that. Clearly if Google is picking up the values, then it is just its prerogative as to what it indexes. It may even just be a quirk of the webmaster tools interface (which I believe we have seen before). Google has always said the sitemap is just one signal it uses and it will still crawl your site naturally, so it's possible it's just not allocating things to the "new" sitemap that it may have seen "naturally".
At the very least, I think we can call this at least a partial fix for the pending issue and can explore any further changes separately.
At the very least, I think we can call this at least a partial fix for the pending issue and can explore any further changes separately.