It appears that once a word is marked as being common it doesn't ever get a chance to become un-common again. This causes a problem for words in early posts when re-indexing a forum: words that appear in many of those posts get marked common when they aren't in fact common when all posts are taken into account.
The tidy() method treats all common words as those that appear in more than the threshold number of posts, but also those that have previously been marked as common ("OR word_common = 1").
There should be a way for words marked common, but now with below-threshold counts, to be marked not-common.
I suspect this might be the cause of many "too many common words" type complaints...