Some sites are defaulting to the webroot folder instead of their own

Could you check what redirect http status code you are getting in your browser? 302? 307?

Is it possible that that root webroot was the default webroot during installation, and then you changed/copied the other websites webroots into this very same folder? Where is/was that webroot located? In Tomcats webapp folder? Or just somewhere outside?

I suspect something is wrong with your tomcat and mod_cfml configuration. How do your config folder in path-to-lucee/tomcat/config/catalina/ looks like? Check all the root.xml files of the respective sites. Check if these are pointing correctly to their respective webroots.