At an engagement yesterday, I ran into an interesting issue where a custom certificate template that was created was unavailable from the Certificate Services Web Enrolment page.
One quick peek into the KB revealed a match for the issue.
You cannot have a Version 2 custom template of Type Minimum Windows 2008 Supported CA to be Available via Web Enrolment in Windows 2008
In Windows 2008, when you duplicate a template, you have an option to select the minimum supported CA. (Windows 2003 Enterprise or Windows 2008). If you want to use Web Enrolment to request the certificate based on a Custom Template created in the Certificate Authority running on Windows 2008, then you would have to create the custom template with Minimum supported CA as Windows 2003 Enterprise.
After we recreated the new template and set it for a minimum level of Windows 2003, all functioned as expected.