I am using the groovy-html.template which generates a link to the build and it is coming up as something like: nulljob/test/2 where test is the name of the job and 2 is the build number. The nulljob part is coming from the concatenation of null root URL and the job URL as can be seen from here:

      <td><A href="${rooturl}${build.url}">${rooturl}${build.url}</A></td> 

The rooturl property is coming from ExtendedEmailPublisherDescriptor.java.getHudsonUrl() as seen here

        binding.put("rooturl", descriptor.getHudsonUrl()); 

This method internally just calls Jenkins.getActiveInstance().getRootUrl() as seen here:

    public String getHudsonUrl() {
        return Jenkins.getActiveInstance().getRootUrl();
    } 

 When I run the above API in Jenkins Script Console, I am getting the correct output:

print(Jenkins.getActiveInstance().getRootUrl()) 

This means, it is not a global configuration issue and from the code it is not obvious how a null value could creep in.