Right - Agents don't always spot it, which is why the "personal touch" (telling the phone/ticketing/gate agent to look for it explicitly) is always the best policy.

It's annoying to deal with multiple PNRs, but sometimes it can help, particularly if you have to change your schedule, or if you're waitlisting for a different flight or class of service on multiple award tickets. For awards, you can grab what's available, then use additional PNRs to waitlist for additional capacity.