The same thing happened to me when I added my most recent line. Added to line with an iPhoone I owned already and when it was time to upgrade, I wasn't showing eligible online.
All it took was a quick phone call to AT&T explaining that that I did not get a subsidy when I activated the new line & I had used my own phone. They manually fixed my upgrade & I had no problems picking up a new iPhone in store the next day.
I'm glad you had luck, it seems to depend on the representative. I had the same issue and multiple customer service representatives said that I was no eligible for an upgrade. Only after I canceled the line and added a new one did they tell me that I should have been eligible for an upgrade. All three of my lines were out of contract and I was very close to switching to Verizon at the time.