One constant thread you see at the forums are threads complaining that their sites become automatically unverified in Google Webmaster Tools. So the webmaster needs to go back in and manually click the verify button in Webmaster Tools, to reverify the site.
One webmaster wrote a Google Groups thread discussing a pattern he has seen. This webmaster wrote a script to notify him whenever his verification file is being accessed by Google. This way he knows when Google has tried to re-access his file and if he needs to go back in a verify the sites again.
Over the course of months, he believes he found a pattern where if he verifies his sites at around 12:22am (not sure what time zone), without failure the verification will fail, even if the verification file is there and accessible. His theory is as follows:
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.
Maybe, at that time, Google's webmaster tools servers hiccup and need a nice kick? Or maybe it is nothing. But I found this thread both unique and interesting.
Googler, JohnMu, promised to show it to an engineer. So I hope to see confirmation of some sort, shortly form Google.
Forum discussion at Google Groups.