That sounds most odd - as far as i know that preference (feature_wysiwyg in admin/features/new) is just like any other and it shouldn't make a difference if it's running on IIS or any other server. Maybe you mean some other pref, as feature_wysiwyg isn't actually on the wysiwyg admin page usually?
Do the other preferences work ok, like Forums of Blogs?
You might get round this by running the WYSIWYG_6x profile, which sets this and various other prefs for you.
The other possibility is that the prefs are set ok but the editor just doesn't work in IIS - not sure it's been tested. Check your server logs for any denied access to files, especially inside the lib/ckeditor directory. The web.config files may not be set properly for this.
Hope something there helps,