Minecraft – Nether Portal never goes to Nether

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).

(Minecraft Wiki)

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.

Break your bottom portal in your world, make another portal up above, then go to the nether with that one. Go to the bottom portal and deactivate it by breaking it, and then finally go back to your upper nether portal in the nether and use it, taking you back to your world.