After about 6 or so days of webmasters not being able to verify their sites in Google Webmaster Tools, Google has finally applied the fix. On March 28th, we reported verification issues with Google Webmaster Tools starting some time before March 27th.
Google was aware of the issue and said there would be a fix soon.
Yesterday afternoon, Googler, JohnMu, updated the Google Groups thread telling us the fix is now complete:
From what I can see it looks like this issue has been resolved. Thank you for your patience!
If you still have problems with regards to verification, please continue to let us know.
So if you are still seeing any issues, please go to Google Groups and update the thread.
Forum discussion at Google Groups.