Originally Posted by Clarrie

Hi Clint

Have several sites on the same WMT account, and had the problem for the first time adding a new site. All the other sites are set up the same, and previously had no difficulty setting the preference, so concluded that its something new in WMT, and went looking for answers.

I came across this post problem setting preferred domain - Webmaster Help

Which sort of makes sense really. Don't know if its the "right" answer, but it was enough for me to leave it for the moment and see if a "real" problem turned up later!