WordPress stats Posts & Pages has wrong links

I’ve recently installed JetPack on a couple of sites I run and started to use the WordPress stats module to supplement Google Analytics. For the first couple of days everything seemed to be working fine but yesterday and today I’ve noticed that the Post & Pages section is almost totally populated with links to 404 pages.

If I look at the links in the Posts & Pages section they are like this:

http://www.naturalborncoder.com/2014/10/27/installing-and-running-kvm-on-ubuntu-14-04-part-4/

but I would expect:

http://www.naturalborncoder.com/virtualization/2014/10/27/installing-and-running-kvm-on-ubuntu-14-04-part-4/

As I use the permalink settings:
/%category%/%year%/%monthnum%/%day%/%postname%/

Is this a quirk of WordPress Stats or is there some deeper problem with my site? I’m new to WordPress in general so is it a bad idea to use custom permalink settings?

The blog I need help with is http://www.naturalborncoder.com.