I have same issue but with an extremely simple project where I am training another staff member about setting up a Map Series, so all we have are the base ESRI basemap, and a polygon layer that is being used to drive the Map Series. The polygon layer has 2 attribute fields, one for map name and one for map scale.
We have made 3 polygons, given them all names, and given 2 a map scale of 1:1000 and one a scale of 1:2000
We then made a Map Series based off spatial and set the options to use the reference scale field for sorting out extent. Coordinate system for the map is BC Albers, same for the feature class driving the Map Series.
However, when finishing the setup and clicking on the map series pages in the Contents menu, the map recenters to somewhere near madagascar and at a scale of over 7 million in a completely unrelated coordinate system. I can re-open the map properties and re-set the coordinate system to BC Albers, and then click on a map series page and it works properly sometimes once, but clicking on another page again resets the coordinate system to something completely unrelated. Map series reference scale field was turned on and pointed to the map scale attribute.
We turned off using the map reference scale attribute to drive scale but no change. Also noticed when reference scale is turned on and it is using the map scale attribute to drive the map series extent, that the scale in the main map window does switch to the proper scale very briefly before changing to the 7 million+ scale and recentering to the same madagascar area.
Currently rebuilding the project to see if it fixes the issue, and will then troubleshoot the reference scale option setting to see if that helps, but so far this bug has totally confused the educational process on how to set up map series'!
