I do remember something similar happening to me, but like it worked after a 3rd attempt or something like that. Have you tired standing on the stone while playing the Ocarina?
When you stand near/infront/behind the stone and get out the Ocarina of Time does the little 'Jingle' come up, that happens throughout the game? Because when you get out the Ocarina at a certain time (Like in-front of the Waterfall to get into Zora's Domain) that little tune plays to indicate that you need to play a song and that its important. I think the tune that indicates this plays when you get out your Ocarina out for the stones of time.
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