User blog comment:Kirkburn/Technical Update: July 1, 2015/@comment-126761-20150703153651/@comment-126761-20150703170204

That's not entirely unexpected - I believe the 'logged in' timestamp is more literally 'when the login action occurred', not 'when was the account last seen active'. Internal bots would rarely need to log in, hence the large discrepancy there. Otherwise, there might be some odd quirks caused by the transition over the last few days - but they should resolve themselves in time.