I would venture to guess that this can easily be explained by different speeds. If the Destiny left at a speed less than the seed ships, it can easily be explained that over the course of the vast amount of time the Destiny was travelling that the seed ships gained distance over it.

Another possible explanation is that although the seed ships travel "ahead" of Destiny, it is plausible to assume that they were simultaneously send to various galaxies. If for example you were travelling to New York City but wanted to stop at every major city on the way(Destiny and the Galaxies on its path), it would take you much longer to reach than if you travelled straight t