The reason your WoW Macros aren't executing is because you didn't give them a possible way to execute. Named WoW Macro Action is the same as WoW Macro Action, except the macro and the Key Combination are configured in this library. Named WoW Macro Action, and WoW Macro Action, are the same as Keystroke Actions, except that they are directly linked to a WoW Macro on that Keystroke. In this case, the bug is that you are allowed to Export this without it having any keystrokes to press!
/click names can be used to execute the WoW Macro from some other WoW Macro. If one is not given, it will be automatically generated internally -- the macro has to have a name either way. The /click name has no use at all, other than if YOU want to put "/click MyOtherMacro" inside some WoW Macro that is running due to some keystroke or actual mouse click.
So each of your macros either needs a Key Combination that is unique against all of the other WoW Macros loaded on the same character. I would generally recommend separating the WoW Macros into Sets on a per-class basis, and then only load the right class's set for each Character. That way you can reuse the same 3-5 key combinations (e.g. because a Hunter won't need to load Mage) instead of 30-50.
The tradeoff to separating the macro sets is that your Hunter will not have Mage loaded, and therefore it will need to be loaded in order to put a Mage in that slot.
Personally I don't switch teams around more than once every 30 seconds so I really don't mind my method of switching teams:
1. Drag a character into some Slot to replace another
2. Export -- this part will generate the ISBoxer Addon with the right toon names from the switch, and it will tell each window to reload ISBoxer settings
3. Re-launch the newly modified team -- this is going to apply the characters that are now specified by the team. This is important, because an Export is just going to tell each logged-in guy to reload (not switch to the replacement character)
4. Do a /console reloadui on all characters that are still in the game -- this reloads the ISBoxer Addon and thus all of its newly adjusted WoW Macros
Takes a few seconds but it's not that bad. Most people don't realize this is possible.

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