Vanilla 1.1.9 is a product of Lussumo. More Information: Documentation, Community Support.
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If you installed the App Store version of Ulysses, the Application Support folder and all Preferences are stored in subfolders of
This is due to the Apple's sandboxing restrictions, where each application has only access to its own data.
It is indeed strange that the selected font cannot be remembered. Is there any Console output?
Also, you could check if settings are remembered if you backup/delete the above data folder.