a few years ago, traveling SEA-SAN-BWI on a 545pm departure, we tried to drop bags ~noon and were told the same thing
I asked the agent if I could check the bags through if I SDCd to the 3pm flight, and the answer was “Yes” … a few minutes later I called in and asked the phone agent to undo the check-in and SDC me back to the original flight
to this day I’m not sure how the system actually hiccuped, but SAN-BWI credited twice