I have faced the issue on many occasions. Earlier I used to bang my head facing this issue as it never allows to edit the macro seamlessly. This seems like an issue with App Permissions. But, now I never jump to 'All Configurations' windows and search the Macro there, instead I visit Advanced Search >> Macros.
What I assume, when we jump to Advanced Setting from the Current app, it sets the context of the app which is selected and if the macro has permissions restricted to a particular app, Splunk will not let you edit the configuration.
So, I always prefer, Advanced Search >> Macros way.