I once booked a stay directly thru Hilton, for an outrageously low rate at a normally very expensive property (for obvious reasons, I'm not disclosing details here). It wasn't a prepay, and there was nothing on the rate that said I wouldn't get HHonors points.

When I was checking in, the clerk looked at my rate, was a bit astounded, and said that she's deleting my Hhonors number from the record, because "that rate doesn't qualify for points." I protested a bit, and she told me that "the very low rates don't qualify for points" and that mine was obviously in that category. She didn't look like the type who could be argued with, it was late at night, and I was the only person in the lobby wearing a t-shirt and shorts, so I didn't bother.

Anyway, as soon as I checked out, I faxed the hotel folio to the Hhonors service center, and was promptly credited points for it.

The lesson to be learned is common on FT: try, try, try again. I've never done a Priceline/Hotwire hotel, but I'm sure many have had luck with a similar tactic.