Upgrade still waitlisted even though R class is available

I am waitlisted for an upgrade on an international flight using a GPU and expertflyer shows R class availability.
I thought R class availability happens only once the waitlist is empty. Why don't I get upgraded?

I can get a confirmed upgrade if I buy the upgrade using miles and cash on a cheap fare, but not using a GPU on my B fare.

Is this a mistake or some new rule I am not aware of?