We have recently installed a new Comodo SSL 3-domain certificate for our PHP-based wesbite, as a replacement for an expired Comodo cert.
The website has a login area - currently, users cannot login at the SSL-protected website using Internet Explorer any version (incl. IE 11) until the site is added to the trusted list in the browser settings. No error messages shown.
All other browsers work OK. Before we renewed the cert, IE used to work OK.
No chains or troubles with SSL cert installation.
I can’t think of anything off the top of my head that could cause the issue you face aside from being a trust issue. If I could see the affected site(s), then I might be able to better advise. If you don’t feel comfortable with broadcasting that in a public forum, you can easily open a support ticket via the Comodo Support site and they might be able to better advise.