This happens in the non beta version in the realms as well. But my bug, I can go over 1000 blocks away in the over world and when I enter the portal it takes me to the portal that was created first in the nether, then when I come back it puts me in a new portal.
The starting Portal is 1033 66 123, Nether Portal is 127 58 14. I broke the starting portal, went to 527 87 -175 created a portal, went to the nether, that Nether Portal 127 58 14, came out of the nether portal at 1025 66 121. Mind you that the Portal created was at 527, 87, -175, and the starting Portal was broke before creating the new portal. I guess it wasn't 1000 block but it was 500 and that should be far enough away to be in a new spot in the Nether.