It would really help to see your configuration in order to answer this question (see http://isboxer.com/forum/viewtopic.php?f=18&t=13 for instructions). For example, it could be that you chose a Key Combination that is used by something else but sneaks past ISBoxer's detection of duplicate keystrokes -- people like to do this by using right-modifiers in the Hotkey box. That will conflict with the left-modifier for creating the WoW Macro; only one of the two macros will exist. Without seeing your configuration, there is no way for me to rule this out, let alone consider the possibility in response to your question.

The only other thing I can suggest is that you can also look at the lua files generated by ISBoxer, in your ISBoxer Addon folder -- World of Warcraft\Interface\Addons\ISBoxer. Each macro you set up is defined in a character-specific lua file in this folder, separated per Character Set. This would allow you to confirm that the macro you're expecting is listed in the file, and that the Key Combination you selected even translated correctly into WoW's key binding format.