A little insider stuff...
On WIN9x systems, installers create the file WININIT.INI which lies in the windows folder. This INI file has sections which specify files to delete or rename.
When Windows boots up, it checks if the WININIT.INI file exists, and if so, it launches WININIT.EXE which parses the file and deletes or renames files which could not be deleted or renamed during the installation process.
WININIT.EXE is the one which prints the message about updating files during bootup.
All this applies only to Windows 95/98 however.