Post install changes not being saved

I am using MSIX for the first time to package up an exe, and having an issue getting the application config choices to save correctly and to include them in the deployed installer.  I am starting with a clean vm and selecting the .exe as the source file, the last step in the install process launches a configuration editor which creates application customizations.  Once I wrap everything up I check that the application did install correctly with the customizations required.  When I then install the msix package to another machine the core application is installed correctly but with none of the customizations I setup.  How do I go about troubleshooting this?  Thanks for all your help.