Before you say this is a duplicate, I am well versed in the normal operation of portals, and understand how to link portals that are very close to each other. This problem is occurring in spite of my understanding.
I have two portals - the main access to my base, at y=66, and a portal which is supposed to take me to the top of my mob spawner tower, which is at y=230+. I've calculated the exact locations for each portal in the nether and placed them accordingly, but no matter what, the portal that is supposed to take me to the top of the tower just spawns me at my main overworld portal. I tried raising the tower portal in the nether slightly in hopes that that would help, but it didn't.
Coordinates of main portal pair: -3653, 66, -2722; -456, 70, -340
Coordinates of tower portal pair: -3736,, 238, -2739; -466, 77, -342
It seems like these should be far enough apart to link properly... Any ideas why they aren't? I hope I don't have to raise the tower portal a lot, that would defeat the purpose...
Images showing relative locations of the portals: