I suspect it's an aircraft swap, either into or out of the GATx fleet, which changes whether 1D and 1F exist on your flight.

If you had been minded to hold on, then the agent should have rebooked you to other seats without charge, the additional charge here relates to the higher cost of advance seat reservation after initial booking. It's not clear what you ended up doing, but they would probably refund the additional seat fee after the event if you submit that via the relevant form, but the usual process is to call up.

By all means use this forum to check things out first, it may save you some time.