How are you sending it from another window? Where is the macro? What keybind does it have?
When sending keystrokes to the game, with modifiers, from another window, the behaviour is exactly the same as when ISBoxer is used to send keystrokes to any other game windows. You have a mapped key, with a hotkey, and that has a Keystroke Action which sends the Keybind combination to the Target windows, which then receive that Keybind Combination and process it as per normal.
If you don't have a mapped key which is collecting your hotkey you are pressing, then that just falls through to the current window. I.e. if you are pressing CTRL+T on your main, and just expecting that to go through to the slave windows, it will not, unless 1. you have a mapped key with CTRL+T as a hotkey, or 2. you have broadcasting enabled. Now there is also a difference here too. If you had a mapped key with a hotkey, you could press CTRL+T, and it could be sending CTRL+T to the game (a straight key broadcast), or it could be sending CTRL+ALT+SHIFT+P (a key remap - usually used to make complicated keybinds easier to press, and mostly as part of larger rotations). A straight key broadcast is just that, it is like having broadcasting enabled, but only for certain hotkeys/keybinds, because most of the time, you don't want broadcasting enabled on everything (like movement keys, because your toons will run away from each other).
So. If there is a problem, it is most likely in your isboxer config. Which you can share if you need help with it.
http://www.isboxer.com/wiki/Configuration_SharingIf you do share, provide info like which character set, which character is the main, which hotkey you are pressing, and which toon should be receiving what keybind.