Soo...I understand that the portals seem to mess up a lot. If you make a portal in the normal world, it makes a portal in the nether, but sometimes when you go back through the nether one, it makes a new portal in the normal world. This is due to the nether portal having to be offset from its real location because of an obstacle (like a mountain).
I've discovered another way for a similar glitch to happen. I built a portal in the normal world (portal A), which made a portal in the nether (portal :cool.gif:. Later, I built another portal a good distance away from the first one in the normal world (portal C). This portal, for some reason, linked up to portal B, rather than creating a new portal a shorter way away from it. I didn't know the glitch could happen this way! I was almost sure I was far enough away. What could be causing this version of the glitch to happen?