Thank borgus1. All my drivers are up to date and this has been an ongoing problem for me for a while now. I think I would have done 3 or 4 video driver updates in the time I have been experiencing this.
This morning I may have solved my problem.
When I produce my videos I click on Intelligent SVRT to determine the best profile for me. I then just click start and off we go. This morning I notice that before I hit start the "Hardware video encoder" box is ticked. This time I ticked SVRT which unticks Hardware vide encoder. This has produced the video and all the 3D Transitions are working! Maybe some one can explain that to me.
Also I notice the first version where there are no 3D transitions is 2.45GB and the successful one is only 2.29GB. Both the same length and both the same profile. That's very strange as well.
Hopefully I have tripped upon the solution to my problem although I don't really understand what has fixed things for me.
Thanks for your help.