I'm guessing that it just moved later to allow more possible connections. FL396 now departs ATL 10:20am arrives SFO 12:35am.
(They made similar moves on west coast flights out of MKE)
If that's too late flying the evening before is an option.
An easy way to poke through the schedules is http://aviability.com/flight-search/...-united-states
It appears come fall the departure time starts getting earlier... Oct back to the original times. Suggesting maybe summer loads need those extra connections to fill flights?