Map Tour Integrated Layout and web map extent

[KelleeKoenig]

I have a web map of points distributed globally, and when I try to use the Integrated Layout many of the points are "off" the base map rather than having it pan.

This does not appear to be an issue in the Three-panel Layout.

Is there something I need to adjust?

[GregoryL_Azou]

Yes you will need to adjust the Map initial extent.

When you switch from three-panel to integrated layout the initial extent isn't updated so some of your point may appear under the media panel. You can adjust the initial extent through the builder Settings dialog (extent tab).
When you use the three-panel layout, the extent you define there will define the extent for the map visible part, so your points won't be hidden.