So, as noted here. http://www.isboxer.com/wiki/WoW:Macro
So your current configuration is effectively excluding all the non ATG member options at the time of Export.Conditional Macros
Conditional Macros are those that may include or omit lines depending on available conditions. Conditions are resolved at the time the ISBoxer Addon is generated, when you Export to Inner Space.
Why? well, because ISBoxer only sends Keystrokes and mouse pos/clicks to the game, it does not push info to say you are in ATG BlahDeBlah, so the resolution of your macro is done at the time of export, and any unmet conditionals are removed from the macro. Why does it not send ATG info?? Because WoW does not have an open interface that ISBoxer can shove anything it likes down it. It can only send Keystroke and mouse info, via the standard Windows mechanisms (to do otherwise is a clear breach of the EULA/TOS), so WoW has NFI that you are in ATG Mage-Fire, it just knows that you pressed the appropriate key combination.
You need to change that way you are configuring ISBoxer. You should have one or more Macro Sets, and assign those based on spec (if needs be). If a character can change spec mid session, then they need to be assigned both macro sets (the only restriction being that assignment of multiple macro sets will need to ensure unique key combinations across them). There was a discussion on organisation of the Macro Sets here http://isboxer.com/forum/viewtopic.php?f=4&t=6561.
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