We have many users that use iNotes with IE, and the “iNotes Warning…” has become an unwelcome yet familiar sight. However, recently we have had luck with disabling popups for the site (holding down the CTRL key while clicking can determine if this will work for you). In some cases you may have to go so far as to uninstall one or more Google-type toolbars which have popup-blocking.
It’s not perfect, but it tends to work!
HTH!