I called in and they had no clue. They say it's showing me as checked in for the first flight, but not checked in for the second. Transferred to online support and they couldn't get it to work either. The only thing we were thinking was that the splitting of my RUC to only be applied to the first leg might be preventing me from checking in to the second leg until getting to T-24. Initially I tried checking in to the flight 24h in advance of the first leg, but I'll need to wait until around 4pm ATL time to try again for the second.