Better hardware and the latest SQL Server release does not always mean that things will run faster.
With this exercise we have effectively increased performance at the expense of maintenance. Well worth the change.
It turned out that the issue was not Hyper Threading related, but a Bios misconfiguration instead.
We were able to tune the offending processes and go from 85% sustained CPU utilization to almost nil.
Over 3 weeks ago we solved the issue we were having with one particular cluster node running SQL Server 2008 R2. We have been going back and forth with Microsoft to obtain an explanation on why the erratic behavior of the RDBMS engine.