If you get a message saying "Setup cannot continue because some system files are out of date on your system." and asking you to update the files, click OK. The new version files will not hurt your system. If you continue to get this message after clicking OK, click the following link for assistance.
Installation Assistance
The only other message that should occur during setup is a message informing you that your current version of a file is more recent than the installation program's version. In this case, always keep your more recent version.