Yeah, just go back later and you can then checking for the second flight (48hrs before it's departure). I admit I was thrown by this at first - in the past with other airlines I have been able to through-check the whole journey in one go. Perhaps this is something to do with the limit being 48hrs rather than the "normal" 24hrs? Maybe that's why many airlines still use a 24hr checkin window - so that connecting flights can still be included even if they are >24hrs but <48hrs in the future. Just a thought.