So I guess the real question is, why would it be that way? Is it a failsafe, like "oops I fucked up and fed it the wrong berries, let me reset it by feeding it the wrong berry and then try again"? If the message is given or not given simply because of a rng element thrown in to make players grow/consume more berries, then it makes no sense that a fruit failing to give you a message should overwrite the fruits you already got messages on.
One possibility is that not getting a message might not actually be just a null thing. If it was given a message, it could be "your chocobo stops growing new feathers".
Now I want to know if you feed your choco some fruits and get message, then feed it one and not get message, then feed it again and get message, does it wipe out the effects of the first berries you fed it before no message?