I have a little script in my verification file that sends me an email
whenever it is being accessed.
My server has a deadish period nightly about this time, for about an
hour. I call it the witching hour.
All or most of the sites in my Webmaster account appear to get tested
for verification every weekend, around this witching hour. And every
weekend all or most of them fail to be verified.
If I reverify at a later time all is OK.
Yesterday I was pressed for time so I only reverified one site. It
went through right away.
All my verification files from all my sites got requested en masse,
some 2-3 times. I got all those emails tumbling in.
Yet only the one site I specifically requested to reverify got flagged
as verified OK.
Tonight I tried to verify one of the others - due to it being the dead
hour, it came back as unverified. Yet the verification file got
requested OK, twice in the same minute (I got 2 emails from my script,
same timestamp to the minute: 12:22am). The site remains unverified.
I know if I try this at a different time, it will verify with no
problem.
So I'm suspecting there's a bug or feature involved.
Since the file is obviously there and accessible, the only thing may
be a slower response time. Even though it responds fully (I get my
email), maybe Googlebot Sitemaps finds it a bit slow and flags it as
unverified.
At least I can't think of anything else.
404 responses are also fine.
I wish Webmaster Tools would be a little more verbose on the reason it
claims the site is not verified at these times. What phenomenon does
it think it's experiencing to decide that?