minecraft-java-edition
The SMP server I play on just updated to Minecraft 1.6.6. We were all really excited about the Nether.
However no matter how many portals we make, when you leave the Nether and comeback to the real world, you end my house (my safe of all places). These portals are not close to each other, but they still connect.
It has become so common for people to exit through my house that I had to give directions.
How can we fix this?
Just make sure there's at least a 1025 blocks distance between your overworld portals:
Likelihood of 2 overworld portals linking to the same nether portal - Normal World portals that are within 1024 distance of each other on either X or Z axis are almost always going to link to the same Nether realm portal on initial construction because 1024 translates to a distance of 128 in the Nether Realm, and the game checks for existing Portals within 128 "radius" around the destination (the 257x257x128 box).
You should also note that, in SMP prior to 1.6, portals were bugged for quite some time and needed server mods like Bukkit in order to work. Ask your admins/operators, there may still be some Bukkit plugin running on your server handling the Nether.
This is how it works:
Every time you enter a portal, the game looks for an exit portal inside +/-128 blocks square (y is irrelevant). If you enter a portal at x=100, y=60, z=200 in the overworld, this corresponds to x=12, y=60, z=25 in the Nether. The game scans a square from (x=-116, z=103) to (x=140, z=153), for all y values from 0 to 128. The closest portal in that space is where you appear. If there is no portal in that area, one will be created in a suitable place. Since there is a chance the x=12, y=60, z=25 will be obstructed, the game will search for an open space in that +/-128 blocks square. If such space is found nearby, all will be good, the new portal will lead back to the same one in the overworld.
Note that the game will only scan within the map height. That means that if you place a portal above the nether ceiling, it won't be found, and the game will create a new one for you.
However, sometimes the game will put the Nether portal far from the starting point, if it can't find other suitable place. Let's say it puts the Nether portal at x=80, y=60, z=110 (this is still in the +/-128 bounding box). When you enter that portal the game will search the corresponding space in the overworld: starting from x=640, z=880, it will search the +/-128 blocks - from x=512, z=752 to x=768, z=1008. As you may notice, the original overworld portal is well outside this box. So the game will create a new portal in the overworld. This is what is happening in your world.
To fix that, write down the coordinates of the portal in the overworld (use F3 to get them) and divide them by 8. Enter the Nether, go to the calculated coordinates and create a portal from the Nether. You don't have to be exact, as long as you are within 16 blocks from the calculated coordinates (you need to match only x and z, y is irrelevant). Then the game should find the original overworld portal. Or: Move the overworld portal using the above logic.
In described situation, there is no way to make the two portals lead to each other without moving either of them. I'd move the nether portal and if the new position is outside of the fortress, I'd build a short safe walkway to the fortress.
Here is a crude drawing of the process: 
Best Answer
Most likely you need to take the time to properly align the portals in both worlds. It takes some effort, but if you exactly align your portals everything seems to work correctly on the SMP server I regularly play on.
From the Minecraft wiki.