Yes. You cannot have a windows service interact with a user's sessions. Ask yourself the following questions:
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On what user session the service should start the application?
What if there are multiple user's logged in?
Does a windows service really need to know about a user, afterall it's a service not an application.
You want to create a scheduled task that is set to impersonate a user and start an application. You will also want to set it's schedule to manual, then invoke it from the mobile app.
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Good luck.