Southwest's tagline should be "Glitch."
This is a known issue that started yesterday. It's unlikely it will be addressed until (at the earliest) Monday. Apparently they don't have IT staff working on the weekend.
A-Listers are allowed to board at the end of the A group, but without "A-List" printed on your boarding pass it's tricky. Reports are some Ops agents aren't allowing it unless you show your A-List card.
Gate agents are saying they have no way of comping Upgraded Boarding, but advising purchase and reaching out to Customer Relations after travel is complete to request a refund.