It has something to do with MultiVerse...
I have had this problem since The End released. Only once has my The End spawned near the central island. What I do is I use DynMap to show where the island is and then I either use world edit to //stack a bridge to the main island OR I just /gamemode 1, fly there and do a /mvp create portal2 p:portal1 at the island and do a /mvp create portal1 p:portal2 at the obsidian spawn point inside a oversized obsidian portal frame.
If you need help, let me know and I can give you a hand.