The non-www one Google did that all by themselves quite some time ago, hence the problem. I didn't put it into WMT. Strange.
Simply put: http://example.com/ is non-existent, so they can't crawl what doesn't exist.
AFAIK that isn't the real issue. I have 301 redirected all other url forms to the correct ones and yet i see those google notifications for both the domain versions. Similar notifications were received by several other people I know.