Dennis from the Google Webmaster Central team informed us in a Google Webmaster Help thread that now, if you have comment code or extra HTML in the verification file used to verify your site in Google Webmaster Tools, it will allow you to verify the file.
I guess some web servers added HTML to all files on their servers. Including the verification file used by Google to verify your site with Webmaster Tools. For example, take a look at this file, you will see this added code:
Now, Google said, even with that added code to the file, Google will use the file as proof that your site is verified in Webmaster Tools. This changed should be working as of yesterday.
Forum discussion at Google Webmaster Help.