There isn't any entry in the Custom Beep window, is there? Any gif animation on any commands? Carefully compare the properties of a button that does beep with one of the buttons that doesn't. Do they have the same theme? That's all the guesses I can come up with.
A good answer is easier with a clear question giving the make and model of everything. "The biggest problem in communication is the illusion that it has taken place." -- G. “Bernie” Shaw