After clicking save, then close. Usually, after clicking close, the GSE main window pops up, but if it doesn’t. The most recent changes to the macro are not saved.
Going to leave this here, figured it out. My Black Ox statue was keeping me in combat, which creates all kinds of havoc for the mod saving.
Hope this helps someone else.
Yep GSE can’t update your macro while you are in combat so it puts that save into a queue which checks are you in combat. You can see the status of the queue by looking at the minimap icon or adding GSE to an LDB panel.