I'm staying at a Fairfield Inn at a negotiated rate (I negotiated the rate myself

). The paltry points post very quickly - my points from last week posted by Wednesday of this week.
If you don't see them in your account within two weeks, I'd call customer service in SLC. You can try the missing stay route (not on line - you have to fax in the sheet) but I've had better luck phoning in.
When I do that, they typically call the hotel directly (they will have your records in their computer) and verify it on the spot. Problem solved.
Don't let it get too far in arrears (several months) or it might be a tougher sell.