I have a script to create separate plots and was using the Application Builder to combine the plots in a new layout. However, most of the plots don't appear in the report window of the application builder. The plots that don't appear have a by column, so there are two plots in the new window. The plot that does show up is a single bivariate plot, but it is still embedded in a new window command. I am using JMP 12.0.1 and am not sure if this makes a difference.
Application Builder scans the open windows for stand-alone reports that it can turn into a script within Application Builder. In general this should include reports include By columns - they will be imported as a single object containing multiple plots within the application.
The issue may have to do with other content that you have added through the scripting. Reports may be excluded if it looks like there is content that is not part of the report. One thing to try would be to run Script All By Groups > Redo Analysis from the red-triangle menu to get a window containing nothing but the report that you want to import.
If you have a script that you can post or other details about what is included in the window, I can look further at why your window is not supported.