Upgraded at counter – not receiving Krisflyer miles?

I upgraded one of my legs on a flight from economy class to business class at the counter for Singapore Airlines (and paid ~$ 1200 USD for that). I’m trying to go back to claim missing miles, but they are telling me that since it was a “last minute upgrade” that I am not eligible for business class miles.

This seems shady…can anyone help me confirm that this is true?