I'm having a similar issue where I have my portals in the proper X and Z for both the nether and overworld. When I go through my portal in the nether world I arrive at the correct portal in the overworld. However, once I go back into the nether through the portal it would send me to the correct x and z coordinate but the Y-axis is wrong.
Also, portals in the nether are not generated like normal (when there isn't one in place) if going to an already existing portal from the overworld. The player may load into the nether inside a wall and suffocate seemingly at the correct x, z coordinates.
I'm having a similar issue where I have my portals in the proper X and Z for both the nether and overworld. When I go through my portal in the nether world I arrive at the correct portal in the overworld. However, once I go back into the nether through the portal it would send me to the correct x and z coordinate but the Y-axis is wrong.
Also, portals in the nether are not generated like normal (when there isn't one in place) if going to an already existing portal from the overworld. The player may load into the nether inside a wall and suffocate seemingly at the correct x, z coordinates.