Never mind, just saw your updated FAQ and the notice about the caching. Once I cleared that up, things worked.
Any chance you’ll give people the option of using the various verification methods? The API allows file, meta and analytics, since some GA plugins already have the analytics verification going, could you perhaps give that option? or allow the option to use the FILE verification, the file verification would probably be easiest to implement, though probably insecure in some environments, but it would take care of the caching issue :).
Or just put a note up saying CLEAR YO CACHE FOO! right on the “Start Verification” thing.
In our case, it was the static nginx cache that caused the issue, which most of our clients would not be able to clear themselves.