If it's the settings under the Configuration menu that you're looking for, then those will only appear if you've run the install sql file. (But don't run it again repeatedly else it will wipe out any data you've already collected.)
If it's the menu option for the reporting screen or for editing the referral source "choices", then read on:
For v1.3.x, the menu is driven by the files in the /your-renamed-admin/includes/boxes/extra_boxes/ folder. If you didn't upload the file for that folder, then the menu options won't show.
For v1.5.0, the menu settings will be automatically installed as long as you load the /your-renamed-admin/includes/functions/extra_functions/ files.
Of course, both versions require that ALL the files in the plugin be uploaded to their respective locations. So really, targeting specific files is moot. If you're missing files from the correct locations, you need to fix them. That's a pretty basic factor with anything on a website.
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