I had a bit of a scare Thanksgiving when I upgraded mom on a cert at the CTO. It was noted in the PNR, but upon checkin (at the LAX Shuttle 1K checkin) the inexperienced agent couldn't find the note in the record. She had to call a supervisor (and subject to 5+ minutes on hold while our flight is boarding). It did clear up once the supervisor checked, however.
I say she was inexperienced because while on hold she also asked for separate 500 mile certs from me for LAX-SFO (1k comp), SFO-ORD and ORD-STL rather than totalling LAX-STL. I politely explained to her why my way was better, and she finally concurs after checking with another agent who happens by. I hope she learned a thing or two, as I had!
