If it's configured like you just said, and it's in a Key map that is assigned to your Character Set, and the Hold option is NOT enabled for the mapped key, and you Exported (from ISBoxer), it is definitely sending Alt+1.

It could otherwise be related instead to the macro itself? Not sure. You could just put /cast !shoot on an action bar and assign that action bar button to Alt+1 in WoW, should work fine.