There has always been a certificate warning with regards to the AKO/DKO portal. In IE version 6 this message was a pop-up that gives you details about the certificate and the warning and what it is for; and clicking the ‘yes’ button would simply take you in to the portal.
This is the same case with later versions of IE, however with version 7 or higher Microsoft has chosen to make this same certificate error much more alarming then in previous versions. Clicking ‘Yes – Not Recommended’ will take you in to the portal same as it has before with no interruption or difference in service because of this warning.
To prevent the page from appearing, you will need to install the DoD Root Certificate. Check WHAT IS THE DOD ROOT CERTIFICATE? for information on how to get the DOD Root Certificate.