Answer
Check the profiles directory under your IFS Home installation path, at repository\server\profiles\ — during installation, the 'Database import and deploy' step has a profile-import checkbox, and if it's checked, whatever profile files exist in that directory get imported into the database, overwriting more recent personalized changes if the files sitting in that directory are out of date. Depending on your situation, you can either clear out the outdated personal profile files from that directory, copy the current/latest personal profile files into that directory before running the installer, or (when the specific delivery allows it) uncheck the profile-import checkbox during reconfiguration or a delivery installation to skip re-importing profiles from that directory altogether.