The bootstrap file is saved in {SpotfireServerInstallation}/tomcat/webapps/spotfire/WEB-INF. If the user running the Server Configuration Tool does not have write access to this location, then the bootstrap file will fail to save. Ensure that the user running the Server Configuration Tool has write/modify permissions to this folder.
Additionally, on Windows operating systems when launching the Spotfire Server configuration tool you may (depending on the environment configuration) also need to right click on the uiconfig.bat and select "Run as administrator".