The fare marketing category and the Qantas frequent flyer earn category don't map directly, even though they have the same names. What matters is the frequent flyer category for earnings purposes.
The first time I ever ran across the upcharge, this was pretty much the reason given. It was taking anywhere up to 30 minutes to fulfil a coffee order.
They may have the same ingredients, but the formulation will probably vary. Shampoo tends to have a lower level of surfactants. In most cases, you'd get away with using a shampoo as a body wash, but using body wash on your hair would be less ideal.
The only thing that happens to status credits is that they expire. If this has happened, there will be an entry on your activity statement about that.
Is there anything in your activity statement?