There doesn't seem to be a pattern for when the glitch is fixed. It seems to be a manual process with no rhyme or reason when it gets corrected. In one case for me, it was fixed 16 hours before departure. In another, it didn't change until 90 minutes before departure. I have no idea how those seats were assigned, but the gate agents were repeatedly calling people to the desk to come forward for their seat assignments if they didn't have one on their boarding pass already. It seemed like it was a mess for the gate agents.

Had I realized this was such a problem and that it would happen to me twice (including one time where I got stuck with the E- seat I was reassigned to), then I probably would have just booked the SFO-DCA flight instead and not bothered. They really need to fix this issue.