I have searched, and it appears as though there are similar bugs to this in past versions. Wordy explanation as I don't have coordinates to work with.
I'm playing in a realm in 1.0.0. The original portal (portal A) I'd built is near the world spawn point. There were no fortresses within a large radius of the portal so I built another one in the overworld, quite far away (portal B). This was about a 3 min powered minecart ride away, so a substantial distance. Portal B connected to the same original one in the nether. When I warped back through from the nether, I emerged at Portal A. I then took one block out of Portal A, and traveled back to Portal B. I went to the nether, emerged at the same point, and traveled back through the portal again - only to emerge at a new portal, near my spawn point but not exactly close to the old one (Portal C). I destroyed portal C and traveled about 2 minutes by powered minecart in the other direction. I made sure to set a new portal up (Portal D) with a different orientation than the others (E-W instead of north south). I emerged at the same portal in the nether and warped back to Portal A.
I'd expect that, like with other versions, different locations in the overworld should yield different locations in the nether.
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Noted. I'll make another portal in the nether and report back with the behavior. If it is as you posit above, I will close the bug. I have another bug that's preventing me from doing this for a while.
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Experiencing the same issue. Win 10. latest build. This problem started with 1.0 or shortly before. Note that in worlds where I had multiple nether portals working as expected before, such that you could enter the nether thru a portal, travel in the nether and exit a different portal to a different location in overworld, now all portals in overworld lead to the first portal created in the nether, and exiting the nether thru that portal puts you back in the same spot in overworld. No fun.
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As @unknown pointed out two portals in the Overworld will be linked to a single portal in the Nether if the distance between those two Overworld portals is lesser than 1024 blocks. This is by design and is not a bug. Here are steps to confirm that things are working correctly:
Create a world.
/tp 0 ~ 0 and create a portal there. We call it Poa.
Enter the portal, which will lead to a Nether-side portal Pna somewhere near (0, ?, 0).
Exit the Nether.
/tp 1023 ~ 0 and create another portal Pob there.
Enter the portal and observe that you still appear at Pna.
Exit the Nether.
/tp 1025 ~ 0 and create another portal Poc there.
Enter the portal and observe that this time a new portal is created in the Nether. The portal should appear somewhere near (129, ?, 0).
3 minutes on powered mine cart isn't exactly "far" in nether. Assuming it was exactly 3 minutes, and your rail has enough power to max out your speed. That puts you 1440 blocks away from origin in the over world, which translates to 180 blocks in nether. The portal search radius is 128 blocks from the mapped coordinates, so if your portal had shifted just by 52 blocks from your original mapped coordinates due to not finding suitable space, then you'll have portals mapping to each other. Although this is a bit unlucky, assuming your times are exact, and your mine cart does not lose speed.
To make absolutely sure that you can't possibly end up in the same portal in the nether, you need to travel at least 2048 blocks in one direction in the overworld, which is the size of a max zoom map.
More information can be found in the wiki: http://minecraft.gamepedia.com/Nether_portal