I mentioned a couple of days ago that the site verification with webmaster central was down.
Having logged in this morning I saw the same warning. As a test I simply re-verified a couple of my listed sites and that seemed to work fine. Then I noticed that there was an erroneous first entry of:
Manage http:///
I selected it, deleted it and wham! all of my listed sites are now successfully verified.
A bug in the system or is google monitoring who actually uses their webmaster central account? Most probably the former!