Anyone else have issues with their flights posting to the correct miles?

Booked a ticket in fare codes AAAIIAAA. Receipt says A, boarding pass says A.

One of my legs was dropped into the "Y" catagory for the miles.

The agent said on the phone since it was a "deep discount" ticket, it doesn't count. For the record it was a LAS-PTY trip.

Anyone else having issues? I emailed my stuff to a few people for a second opinion, they can't see anything. AA's advice? This got me shocked, but two people on the phone said "Do not use our online reservation system, if you're specific on points, call it in, tell us, and we will make sure there is no funky behind the scenes stuff on your ticket".

Or, am I missing something? Seems a bit bait and switch?