I would venture to guess that this can easily be explained by different speeds. If the DestinyDestiny 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 DestinyDestiny was traveling that the seed ships gained distance over it.
Another possible explanation is that although the seed ships travel "ahead" of DestinyDestiny, it is plausible to assume that they were simultaneously sent to various galaxies. If for example you were traveling to New York City but wanted to stop at every major city on the way (DestinyDestiny and the Galaxies on its path), it would take you much longer to reach than if you traveled straight there.