After several years we are now suddently experiencing problems with Google Webmaster Tools "Site Verify", due to supposedly "We were unable to verify your file due to a server timeout." which has been confirmed not to be correct. According to the Official Google Webmaster Help group, several people are expereincing the same problems with their site(s).
Should you use Google Webmaster Tools "Site Verify", you may want to take check-up on your site(s) as well.