It is possible to configure any ISAPI filter as a server-side or site-specific filter. You did not say which option you;ve used.
if IIRF is installed as a site-specific ISAPI, then any new site you install, will not get IIRF.
To change that you need to re-configure the installation of IIRF. Either configure a new ISAPI for each site. Or uninstall it and re-install it on a server-wide basis.
That is the first thing to check - is IIRF configured as an ISAPI for the entire server, or for a specific site?