It may have been they did not know how. They were certainly trying to help.
I booked what I thought was a w fare. Used cr1 at the time to upgrade on the spot. When I look now it says s fare on website though the ticket was $529.
I think the equipment swap messed it up. I had called last week and was told they could not change on to r without losing the upgrades.
Last week I even paid 99 for tod upgrade since I seem to not be clearing many free ones this month. Last year I cleared Orr 95% flying the same places so getting used to this treatment.