I came across this issue while selecting the preferred domain (may be www or non www link of your website) in google webmaster tools. Even though you have added your site to webmaster tools account and verified, when you try to select the preferred domain, you will be asked to verify your website with the below message.
"Part of the process of setting a preferred domain is to verify that you own http://mysite.com/." ....
This can be resolved by verifying both www and non www links of your website..
Make sure you have registered both www and non www links of your website with the google webmaster tools.
eg: www.mysite.com and mysite.com should be added in your website list in your webmaster tools account (this includes the verification of both the links with google webmaster tools).
This is because google considers www and non www links of your website as two different website links.