I have a similar problem , So when you feed your chocobo it gives a message your chocobo changes color in 6 hours and u see a timer on top of ur stable menu , first and second time I did this I got this cutscene where your chocobo changes color, when I tried it for 3rd time to change the color , i fed it and said changes will appear in 6hours i saw the timer i saw the message , then i logged off after feeding it the apples to change his color . I come back after 6 hours and nothing, no cutscene no timer as if nothing happened, and no I never took it during the time .