The "Salesforce1 User" setting only controls the behavior for the browser-based application (one/one.app).
If you have the Salesforce1 User setting ON:
If you have the Salesforce1 User setting OFF:
- User will land on the full site interface when using any browser, mobile or otherwise.
In both scenarios a user can force the Salesforce1 interface in a browser by adding /one/one.app to the URL.
This should have no affect on the behavior of the Salesforce1 downloadable application, which should never launch into the full site interface. Have you tested with multiple devices also? If this is happening I would verify that you are on a supported mobile device or check with Support:
If you are on a supported device for the downloadable application I would verify that your OS is up to date, the Salesforce1 app is up to date, and the app has been fully restarted (double-tap on home button and swipe app up off screen for iOS as an example).
So again, this Salesforce1 User setting only controls which interface you see when you connect from a supported mobile browser. This has no bearing on the Salesforce1 downloadable app behavior which should never show the full site interface.