Build Definition fails to fetch Jenkins Jobs

We are in the process of upgrading to RTC 5.0 and have come across a scenario where the build engine connection test is successful but a build definition that uses it is unable to retrieve the jobs in Jenkins.  This works fine when using Jenkins internal authentication but we are now proving in production scenarios where Jenkins is using Active Directory for authentication.  So the only difference between a working scenario and an non working scenario is the authentication of Jenkins against Active Directory and a new RTC server instance.