Hi Mia -- Thanks for the additional information.
The reason the pop-up charts look different between your screenshots is that the ArcGIS.com map viewer (bottom screenshot in your post) uses the 3.x version of the ArcGIS API for JavaScript and ArcGIS StoryMaps (top screenshot in your post) uses the newer 4.x version. The 4.x version is the latest-generation mapping API that is already being used by some ArcGIS web apps, and it will be generally adopted by other apps in the ArcGIS platform moving forward.
The pop-up charts will look like they do in ArcGIS StoryMaps in any 4.x-based app. For example, if you open you web map in the 4.x-based beta map viewer, you'll see the same chart style (see screenshot, below).
https://www.arcgis.com/apps/mapviewer/index.html?webmap=b3d9a25aa1a748c99b89410eda7a8398
So this isn't an error or bug, it's an updated chart style that adjusts the y-axis range in some circumstances. If you have feedback about how charts look in the 4.x JSAPI you can submit that on their GeoNet community page here: ArcGIS API for JavaScript
Also note that this is not an issue with a particular browser. This chart style will be seen in Safari, Chrome, and other browsers in any 4.x-based app like ArcGIS StoryMaps.
I hope this helps explain the differences you are seeing. Please let us know if you have any other questions or see other issues.
Owen Evans
Lead Product Engineer | StoryMaps