I had the same happen to me. You are talking about your Legacy Chobo right? Picked it up from the Moogle, used the item, but when you try to summon it it shows the message. I had to level up to 20 and get the seals for the Grand Company chocobo so I could use the Legacy. So basically I have two chocobos, the GC one and the Legacy one. I think its just meant to be a secondary mount, you still have to pay to get your GC chocobo. I think if you still have your old character and it's above 20 you can use it right away. This happened to me on a new character.