Nether on Multiplayer is different

I host my own server on my Mac computer. I put 1.6.3 up on my server and checked it out, seemed fine. Went to the nether and the nether seemed to been reformed back to its old form. I have a pics of my 1.6.2 from the portal and 1.6.3. I'm not not sure what is going on and why is not reading the files right. As of right now I can not go to the nether until this is fixed.