Had this problem today on an identical trip to a few weeks ago. Was ok a few weeks ago, but not this time. Airport check-in took forever, and then realized the second flight was only half checked in and the Skyclub had to work to get it straightened out. Now the 4th segment is half checked-in and will need to get fixed. What a mess.
BTW, the Skyclub person said oh you're the second person today with the exact same mileage run iterary that i've had to fix.