Geee...I had the same problem with analytics before but I managed to solve. Just make sure that the code is inserted properly to your page template (if you are using a blog) or website. The placement of code is every important.
But I still can't get answer for my webmaster tool problem. I checked in the internet recently and there seems to be others having the same problem. Looks like it's random and not all are affected. Well, I'm one of the unlucky ones
