I have the same problem with webmaster but I you use Analyses to do that.
Writerpublish.com is a MU site with 6 subdomains.
This is a old site 6 years +. I changed to gmail for work. and that everything up. The joy of one login for everything doesn't quite know what to do when you have more than one.
I was able to set up the new Google analytics I think. I didn't get the filter configured.
I have no analices of Webmaster tools for two weeks.
this morning after setting up Google analytics I'm showing 40 logins with a ratio of 1.2 or three. On somewhat suspicious that and get it all right. normal is for 500 hits a day and an average of 2 to 3 page views per visitor.
I was able to verify Webmaster tools for the means it using Google analytics. I have no memory of how I did it before but it worked for over six years.
I appreciate any help that you can read on the subject