The issue with WordPress.com as a referrer is (probably) related but not identical issue. Several people have had problems with stats changing after the fact that were not during the same period when WordPress.com was showing up as a referrer, which is what Matt was talking about in the post linked above.
I contacted support outside that forum, and the response was basically, "I'll pass that along and we'll try not to have it happen again."
Out of curiosity, was your busiest day sometime near the daylight savings change? I'm wondering if something got messed up with the time change, where those stats for our best days are still counted, just on a different day now. That's complete speculation though.