I had the same problem.. if you played in the original version of FFXIV and had your GC chocobo, go to a chocobo stables npc in town, and choose the option to rename your chocobo, do so, then you should be able to get your bird back. Look under the Action menu, then drag the chocobo mount option to your ho bar.
When you're browsing the quartermaster's stuff, make sure you are looking under the "materials" tab and not weapons or armor. --- Welcome to GameFAQS, where sharing an opinion is a declaration of war. Resurrect the saint from within the wretch.