It is quite possible that there are two different Kingdom Hearts. The KH of the first game can considered, in many ways, the heart of all worlds. The place from which all hearts come and go, the original heart.

In the second game, Kingdom Hearts is created by Xenmas. This project starts in 358/2 Days when both Roxas and (SPOILER)Xion are recruited for that very purpose. Later, Org. XIII uses Sora to continue the task of collecting hearts. It is noted that only the keyblades can harvest hearts.

This theory assumes Xenmas did something to prevent the hearts from going to the KH in the World of Darkness, thus forcing them to gather outside the The World That Never Was. Basically stopping them as they cross from the World of Light to the World of Darkness in the World In-Between (where WTNW is found).