This was my experience this past Monday flying JFK-PDX. I booked on a flight certificate and was only allowed to pay to upgrade to Preferred at time of booking. I called and spoke to 3 different departments, none of which would allow me to pay to upgrade to C+. I have been able to do this in the past without issue.
My flight had 10 open C+ seats listed on the gate monitor. I asked the GA about paying to upgrade as did 3 other passengers on line behind me. The GA would not let any of us pay to upgrade. Flight flew from JFK-PDX with 10 open C+ seats. Not sure what the goal is here but if they don't have enough Medallions to fill these seats, then they should sell them for cash at the gate after a certain point. My flight departed with money left on the table.