Expertflyer shows R7 for this flight so I'd try calling rez and asking a live agent to see if the upgrade can be confirmed-mention you got an alert from an online booking service that the inventory (R) is available so the agent actually checks that rather than just using a command to process and upgrade inquiry/confirmation as it seems there might be some glitch in the system if you are listed for the upgrade but it is not clearing.

The flight also shows C4 and U4 so mileage and or eVIP upgrades as well as free award seats are all available.