What would cause documents not to be recognized the same in FlexiLayout Studio and document definition in Project Setup Station?
The reason for this is the difference in pre-recognition and recognition modes or languages used in FlexiLayout, Project, and Document Definition.
To open pre-recognition settings in the FlexiLayout Studio project, you need to choose FlexiLayout -> Preferences on the menu bar:
In Project Setup Station you may choose Project -> Project Properties on the menu bar and open the "Recognition" tab.
In Document Definition you may use the "Ctrl+T" shortcut and open the "Recognition" tab as well.