Once, I had this Chocobo longer than the two other Chocobo, yet they were both able to breed while that one couldn't. One of the ones that could was even just born recently! It was a fairly stupid situation.
Anyway, I remedied it by running around with the Chocobo. Just run with it for a while, across whatever places possible. This worked for me.
I don't know of any actual time or step count as to how long until it matures.
I struggled with this too... Its been a while but I believe it either takes a day, you have to use it(race with it, w/e), or just plain save the game and turn it for a sec, then go back in... I always found the breeding to be tedious, but it all became worth it in the end...
It is probably because it had just been born and Squaresoft didn't want to encourage pedophlia by allowing you to mate Choco-stud daddy with his own new born daughter / sister.
They had to put a limit somewhere so that players couldn't just mate newborn babies as that would just be wrong and make the mini-game (which is already full of inbreeding) a little less clean.
I don't think they have any time clock or anything on the development of the chocobo, but they may do. The best thing to pass the time would probably be to do the chocobo racing as you have to do that in order to increase the rare breeding success rate ayway so it will speed things up.
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