The Split Timeline occurs because of alternative endings at Ocarina of Time. Not necessaryily two different endings that happen in two different time periods. Let me explain.
As Adult Link, you defeat Ganon, restore Hyule, etc... Zelda sends Link back in time so that he can live his childhood. In this Adult timeline, to me it is assumed that Link DOES not work with Zelda to prevent the events of Ocarina of Time. Thus, the events actually do occur and the storyline continues in the Adult time frame without Link.
The alternative ending is that Link travels back in time and Link and Zelda prevent Ganondorf from ever regaining power. Just keep in mind this is a video game and suppose there is some other way (perhaps the Ocarina of Time as I suggested), that the message was given from Adult Zelda to Young Zelda. Sure Link to did not bring the Ocarina back with him, but it is called the 'Ocarina of Time', perhaps meaning that it has the power to see through time and inherit the message from the future.
Anyway, young Link and Zelda do prevent Ganondorf from taking power and the events of Adult Link never take place. Thus, this is the young Link timeline. Perhaps 'Split' is not the most appropriate word to distinguish the timeline, but it is clear that there are two alternate endings. They don't BOTH happen, but only one happens in each version. Thus, it is not a paradox, but it just spawns two possible endings at which the series has progressed further.
So ya, Majoras Mask does take place somewhere in between the Adult Link and Young Link quest of Ocarina of Time, but you cannot look at it like that. Since Majoras Mask is a sequel to the Young Link ending, where the future isn't known. Remember, the endings don't both occur, only one occurs. If a gamer thinks of the two endings happening simultaneously, that is a flaw in the theory, since they do not. Only one ending can happen at a time.