Delete your addons.txt virtual file? ISBoxer doesn't virtualize addons.txt by default or even mess in any way with your addons or which of them are enabled.

The only difference from running normal WoW should be that Inner Space is running with Administrator permissions, and therefore so is the game. If you're on Vista or Windows 7, and have the game installed to your Program Files folder -- or "Program Files (x86)" -- that means the OS may be virtualizing the file system automatically when not running through IS, and putting the actual addons.txt under something like C:\Users\<name>\AppData\Local\VirtualStore\Program Files\World of Warcraft\. When you run it through IS, with Admin permissions, Windows will NOT put it there.

If this doesn't help, show me your config so I can see what you were doing to addons.txt