As far as the gate checks go - it depends on the airport. I never get checked at SFO in the morning and always get checked at SLC no matter what time of day. ATL is a crap shoot (in more ways than one). As far as the on-line check in being denied you might also take a look and make sure your itinerary is that same as when you booked it. If it has changed and they haven't reassigned seats yet then you won't get an on-line boarding pass.