I have received a reply from support. The ability to manage Hyper Threading on a per VM basis was silently removed in 6.5.
This leaves a bug int he powercli that is not throwing an error when an attempt to make the change is made
This means that hyper threading needs to be disabled on the cluster if you want to get full core performance from your SQL licensing. Leaving it on will mean that you may only get half the performance out of your SQL when using per core licensing.