It is possible that you are encountering one of the "limitations" of the tool, i.e. it doesn't report all identifiers by default. Probably more of a feature than a limitation
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You have two options here: either open the settings dialog and check the "Report on all misaligned identifiers, not only on manually added ones" checkbox, or from the main window, manually add the desired identifiers, by selecting them in the "All available identifiers" list and clicking on "Notify On Selected Identifiers" button.
Once you have a few identifiers in the "Notify on these identifiers" list, you can test the report by selecting the lst file in the first list, and from its popup menu, select "Generate report".
The same report should be generated if the application is started from command line with the desired lst file.
Please confirm all the above, so I don't have to start a bug hunt. Thank you