Well, my checkin worked, thou it have stopped popping up when I first login for the day for the past couple days (since daylight savings change?)
So I had to do it manually.
As a result, it is VERY possible, likely even, for you to end up logged in but not checked in, because it didn't pop up so...

That said, some of you did say that you double checked manually, which should have worked. So there could be an additional bug with it. It might have to do with WHEN you do your check in, thou that's just a guess. To be safe, I'd do it in the middle of the day, avoid, in the very least, the questionable time period between midnight and 5am where things tend to be weird. Of course, you could also be mistaken, but given how many of you there are, you can't ALL be mistaken... probably... unless some are just saying you checked manually because others said it...