When an ocarina song plays on a staff, the notes appearing on the staff are synced to the audio. The purpose of this is to compensate for potential differences in lag or framerate, so that the note always appears when you hear the sound. This poses a problem when frame advancing, because as far as the game is concerned, frame advancing is essentially lag. The note sync mechanic is not robust against severe lag, and such lag can cause the staff to simply stop playing notes, or break in other strange ways.
The Practice ROM circumvents these issues by disabling the audio sync when frame advancing or recording/playing a macro. Instead, the game is assumed to run at a constant framerate with no lag, so that no timing adjustment needs to be done.