I have a custom field assigned to Settings Pages. When I add a new field, the Location changes from Settings Page to Posts. When I try to change it back to Settings page, the change doesn't stick (it stays Post). Also, the new field doesn't save either.
This has happened several times. Max_input_var is set to 5000, so that isn't it.
There are only two solutions -- re-enter the entire Custom Fields set, or delete the Custom Field and restore it from backup.
I restored the backup to another similar site (restored as Settings Page Location), added one new text field, clicked update, and the Custom Fields changed to Post - I'm assuming there's a configuration issue in the Custom Field itself, but I have no idea what that might be or how to correct it.