Not all games party order stays the same regardless of which member you have active (LOTRO is a good case in point for this one). And the party order invite/accept matters. Where the game behaves in a fixed manner, ISBoxer Toolkit generally caters for that in the default config, although it appears it is not in this case. You are seeing the more common pattern of most MMO's, and it is expect you will adjust it as needed.
Now, on to some basic info before we get into some nitty gritty.
ISBoxer is configured from the perspective of the Active Slot (or Window if you like). The Active Slot, is the one receiving the actual mouse/keyboard input. So whenever you are configuring something and you want to say "if window DAOC1 is active do this", in ISBoxer it is always "from the Active Slot do this". Most of the time, it is "from the active slot, send a message to the other windows to press this key".
This can get quite in depth though, because you can have the Active Slot execute a mapped key on another slot, which in turn does something, which might in turn then tell the Active Slot to press a button. Thankfully, you don't do this often.
ANYWAYAfter having a read through again of the chain, if you want to use the method you were originally attempting, I think you probably want to clear your profile settings (File -> Clear), and run through the Wizard and set the following options at the end. These will allow you to use the macros as you indicated for Assist and Follow (or Stick if you prefer). Note: the defaults like to make use of the Number Pad + Modifiers, you can change those.
If you want to also have the "To target DAOC{X}", then untick the "hide unrelated options..." box, so you can set the Targeting table, which in your case might need to be adjusted so All characters press F1 to target the toon in slot 1 (it will be columns of F1, F2, F3 etc, rather than rows).
Although this might not be the boon it sounds as using the above option for Assist/Follow, means there is little use for it. ISBoxer does not currently have a "Target Me" mapped key setup by default, although it would be very easy to create one (this would need to be done manually though as the Mapped Key Wizard does not have an option for it). This is what it would look like.
This uses a Variable Keystroke to have the others target the active slot, and will need the use of the Targeting table from before. ISBoxer will replace the variable {SLOT} with the current active slot number..