Close portals in nether not connecting properly since pre releases

I have two portals in the nether that are close by that now since the pre-release both over-world locations teleport to the same portal in the nether, which wasn't the case before the pre-releases came out.

ex. (from the nether) X goes to X and back, Z goes to Z but comes back to X(Z)

Overworld   Z---------------------------------------------X     

Nether                             Z------------X(Z)

 

Thank you.