When you set up your Character Set using the Quick Setup Wizard, it asks you to enter the names in the order you will log into the accounts. In order for your Action Target Groups to be correctly assigned to the right Characters, you have to be sure to log into each of your guys in the window that ISBoxer expects them to be in. This is the trick that you guys are missing at the moment (and I have a long term solution for this in mind, but not yet implemented).
So.. easiest way to correct this:
1. Launch your Character Set
2. Wait until they're all up
3. From the ISBoxer interface, do an Export to Inner Space. THIS WILL POP UP TEXT IN EVERY SINGLE GAME WINDOW THAT IS CURRENTLY OPEN, DESCRIBING WHICH CHARACTER IT THINKS SHOULD BE IN THAT WINDOW!
4. Read the popup text in each window and log into the correct account in each one
This should solve the apparent randomness. After you've logged into the correct account in each window, it should be stored correctly by the game so you don't have to do this again.

On a side note - I'm not always sure when reading the instructions if your use of "character name" is referring to the username of the account or the character's name of the group of pixels running around the screen.
It's actually irrelevant to ISBoxer for any game but WoW at the moment, since it will use the "character name" in the generated WoW Addon and WoW macros. It depends on how specific you want to be with your configuration for a particular game. For most games, or if you don't need to differentiate between actual Characters, then you can use it to mean an account. For these situations I usually just name them like "EVE one", "EVE two", "EVE three" for example, and then I always use the same account in each of the windows. All that matters as far as ISBoxer is concerned is that they are each in the window that I told ISBoxer they are in, so that any custom mappings go to the right place.