Why won't Webmaster Tools let me set a preferred domain? (says to verify, but it should already be)

If you have both www.example.com and example.com listed in the Webmaster Tools homepage already, try deleting the entry for www.example.com (under Manage site > Delete site) and then re-add and re-verify the record for www.example.com before setting the preferred domain.

If you currently have only example.com listed on the Webmaster Tools homepage, you'll need to add www.example.com as a separate site before you can select the preferred site.

(You mention that you've verified it in the past, but it's not clear from your question whether or not both www.example.com and example.com are listed as sites on your homepage in Webmaster Tools; if they're not, they need to be in order to set a preferred domain. You can delete the non-preferred entry after you've verified and set a preferred one.)

I run into the same problem, added both www and non-www, removed them, added again, verified both with multiple methods, but nothing. Finally I found out that I added https versions only and that is not enough for Google, and after I added both www and non-www with http (so actually FOUR versions of the same domain), finally Google let me set the preferred option.