Chocobo cannot limit break

I have never had a problem with my Chocobo before. I have not had them locked through a bug or had to fetch her from the NPC, so I was not anticipating any problems. Attempted to rank up from 13 to 14 and instead of leveling I got a message saying they cannot gain more experience and my Thavnairian Onion was wasted. I would like to get this problem fixed and my Onion reimbursed.

Time: Around 3am?
Frequency: Only let this happen once, not willing to test again
World name: Goblin
Character name: Myew Mihgo
NPC name: Companion (Nutmeg)
Monster name: n/a
Class/Level: nin(50)
Party or solo: solo
In-game time: no clue. daytime?
Area and coordinates: Lavender Beds, 12,14
Steps:
1. Observe Chocobo has max exp, rank 13
2. Observe secondary confirmation of max exp for rank through having a golden level number
3. Place Chocobo in the FC's Chocobo Stable
4. Select 'Tend to My Chocobo'
5. Select 'Train'
6. Confirm warning message about further training will not result in additional EXP unless the rank cap is raised
7. Choose Thavnairian Onion as the reward item.
8. Watch the training sequence

Result:
Received an error message stating that they could not gain any exp

Expected Result:
Chocobo should increase rank to 14, have its experience reset to 0, and be allowed to reach the new cap designated for rank 14 chocobo.

http://i.imgur.com/a1fW5PO.png

I'm afraid that not only that you'll not get your Thavnarian Onion "refunded" (as it's a replacable / non-unique item) but that you've used it incorrrectly. You can only increase the Chocobo's rank using the Onion while the EXP shows 0/xxxxxxx and not at fulll xxxxxxx/xxxxxxx as your picture shows.

In your current situation, you should be able to take your chocobo out from the stable and kill an enemy to level it up.