The first thing to consider is that Qlik NPrinting generates one report for each Newsstand user. For this reason, there will be one file for each user, and not "just one", in the Qlik NPrinting Application Data folder. Those reports may be absolutely identical.
As for the setting apparently being ignored, by default runs the check to delete old reports once every 24 hours. If no new report has been run in the meantime, the old reports will not be deleted, even if more than one day has passed.
Should there be a feeling that the periodic check is not run, the settings can be enforced:
The first setting is the recurrence in seconds (default: 30 minutes) for the task that will check for reports in the newsstand and unlink the older ones. The second setting is the recurrence in seconds (default: 24 hours) for the task that will scan and remove the actual files, after checking that the conditions about days and reports to keep, plus the presence of newer reports that supersede them, are met. In this case, we would change the default value to a shorter time (43200 seconds, 12 hours) to make sure the task is run more frequently.