I've found in the past where DL.com shuts off longer connections from being booked even though they are perfectly valid. The several hour overnight in ATL comment in the OP leads me to believe this might be it.
My recent example is a connection through ATL with a 2 hour layover would not come up on DL.com because a 1 hour connection was available, but the 1 hour connection was higher because inventory was unavailable out of ATL (same outbound flight). Had to book through an OTA instead.