I found the same thing to be the case. Some gate agents (and even some rewards desk agents) don't understand the rules.
Earlier this year, I was flying from LAX-IAH-CLE-ORD on a full Y ticket (all travel during the same day) and the reward desk person told me it would be 5000 miles per segment.
Needless to say I hung up and called back. I got a more knowledgeable agent who charged me the correct mileage.