I am trying to use the publisher extension in ArcGIS Desktop 10.5.1 with our enterprise geodatabase layers and I am getting 2 different data sources when I open the ArcReader document created by the ArcGIS Desktop Extension. Everything is supposed to be stored in the data folder which is created by the publisher extension but it doesn't work. I've worked with an ESRI Analysis and we couldn't figure out why our connection sources are in 2 different locations. I will provide the screen shots below. Has anyone had this issue? I would like to start using the ArcReader with a few service people in our office.
ESRI tutorial Link: