Actually since he used the wizard, it doesn't matter if Ctrl 1-=, etc are bound. The FTL modifiers are only applied to the 3 specific keys -- follow, assist, and target. With the method used by the wizard, you CAN have Alt+1 broadcast Alt+1 (etc) with FTL auto-assist, and it will work just fine

Instead, what I would assume is that the wrong character is logged into the wrong window, so ISBoxer is incorrectly assuming which one is the current character. If all of your accounts arent merged into the same battle.net account, you can just fill in the account names per Character -- the wizard does this for you, but it would appear that your ISBoxer characters were not generated by the wizard.

If they are merged into the same battle.net account, you will need to make sure you're logging into the right character in the right slot (because support for this directly in ISBoxer has not been added yet, since battle.net accounts with multiple sub-accounts has an additional field required). There's a number of ways you can do this.
1. The name of the character is always shown in the taskbar buttons and window titles. On Vista or later, if you hold down alt, and hit tab multiple times, you can see the names of the windows in the alt+tab preview window thing...
2. When you log into the game, the first thing ISBoxer does is say which character it thinks it is, in the chat window. Look for it -- if it doesn't match the one you're playing, then that's going to be a problem
3. When each window first comes up, it says which character it should be, with popup text
4. Each time you Export, it says in each window which character it should be, with popup text

I'll be working on improving this more, since this still comes up even with ISBoxer setting up account names in config.wtf for you (particularly in cases like this one where either the names are not filled in in ISBoxer, or they would all be the same battle.net account anyway)