Recently I had booked a circle trip from SJC to ATL, ATL to PHL, and PHL to SJC on a Skymiles award. I then purchased a separate roundtrip ticket from ATL to SAV and SAV to ATL so as to connect with the first two legs of the Skymiles ticket. The reason for this was that the Skymiles ticket allowed for a stopover only if it was "on the routing". That allowed for a stopover in ATL but with our destination being SAV, we needed to purchase the extra "side trip" ticket.

The point of this posting is that when I checked in at SJC for the SJC/ATL leg, I tried to also check in for the connecting leg ATL/SAV and was told I could not do that since it was booked in a separate record. Thus, I had to wait until reaching ATL to check in for the ATL/SAV leg. The same thing happened on the return - checked in at SAV for the SAV/ATL leg but had to wait until I got to ATL to check in for the ATL/PHL leg.

What makes this even stranger is that in SJC they were willing to check my bags through to SAV even though I wasn't checked in for the second leg, and in SAV they were willing to check my bags through to PHL.

Does anyone understand what the explanation is for this oddity?