Arline passenger records have two fields for a passenger's frequent flyer number: one for crediting the flight, a different one for the flyer's status with that airline (or, in some cases, a partner) for privileges.
The problem is:
- Many (most?) airline agents don't know this.
- If they know this, they don't know how to enter them both correctly.
- If they know how, with 200 people behind you in line they can't take the time.
- If they can take the time, they make a mistake.
Best to follow Mwenenzi's advice and claim retroactive credit separately for each. That doesn't necessarily mean missing out on the benefits of status, though. Have some other evidence of your status, such as the airline's smartphone app, ready to show. You will not be the first passenger whose elite status wasn't printed on a boarding pass. It happens for many reasons. Agents are used to it. It may take you ten extra seconds to get the benefit, but you should get it. (If one offers to enter your number into the computer and print you a new boarding pass, decline. You can offer to explain why. Chances are they won't take you up on that offer, especially if anyone is behind you in line.)