Without this plugin using End portals in strongholds works just fine.

With this plugin all End portals send you to the End, but you retain the same location as the portal you used in the main world.
If the end portal in the main world is X:-847 Z:50, you will appear in the end at those same coords.

http://multiverse.github.com/news/better-end-support.html

I have found if I set the scale for The End to 16 I get teleported to a spot on the world instead of in the middle of no where.