Sounds like you're not using macros in-game on the /following toon to properly target the enemy.
Two simple solutions:
Have a key with this macro: /target nametarget (where "name" is your main character). Press that key after you target a new mob to have your /follower now target that mob, then continue on with your attacks.
Or..
For all /followers, change all your skills/spells to macros like this:
/target nametarget (or party1target, or focustarget.. depending on how you set up your macros)
/cast skill

Multiboxing is more than just loading up an AHK script. You have to configure a ton of in-game macros to properly target and use skills. The AHK script simply sends a keypress to all instances of WoW.

It doesn't matter where the WoWs are running from, as long as they are already running from the same computer when you kick off the AHK script.