RSFirewall! alerts that many Joomla! files have been modified

I have just updated my Joomla! installation and RSFirewall! alerts me that a lot of files have been modified.

This problem is most likely generated because you have used ASCII transfer type when copying the new files to your site. In this case the files will not be transferred correctly and will be marked as modified by RSFirewall!. The correct transfer type is Binary and it should always be used when copying new files on your site.