That's one of the frustrating aspects of online check-in for trips with same day or other short turnarounds. WN, to its credit, allows its customers to book two one-ways for the same price as a round-trip, which solves this problem as you can check in for each flight separately at its respective 24 hour window. I understand why most airlines are unwilling to price one-ways exactly at half the price of a roundtrip, but I wish some other workaround was available to allow the outbound and return segments to be divorced for purposes of checking in as early as the second the check-in window opens.