I'm on Masamune with my Legacy character, but I never had a chocobo in v-1. But since I get one anyway for being a Legacy member, I did notice I couldn't use ANY mount - not the legacy chocobo NOR the coeurl mount - until I had joined the Immortal Flames.

You have to progress through the main story until you decide to join one of the three Grand Companies. Then you head to your GC's Quartermaster in your home city. Mine was the Immortal Flames, so I have to report to Ul'Dah, next to the Aetheryte crystal room.

Talk to the Quartermaster and then in the window that opens up, look for the three tab/buttons. There's Weapons, Armor, and Materials. Click to Materials.

Look down the list for Company Chocobo Issuance. It will cost 2,000 company seals.

Once you have the Issuance, take it to your city's Chocobo Master and give it to him. He'll give you your Chocobo and you'll have to name it. After you've named the chocobo, you talk to the Chocobo Master again and he gives you your rider's license.

YOU NEED THE LICENSE TO USE ANY MOUNT. As soon as I had my License, I could use my company chocobo, my Legacy chocobo, and my Coeurl mount and they've worked fine ever since.

Character Name: Ariana Deveraux
World: Masamune
Class/Level: 33 Paladin
GC: Immortal Flames

By the way, for all my Masamune Legacy guys who speak English, I have a Free Company called Archangel's Wing. Looking for members. ^.^