I shot a sequence last night in portrait mode. when importing via LRT 6.1 the images were shown in Landscape orientation, then when LRT ran the wizard they switched to portrait. The 'drag to lightroom' import shows them in Lightroom in portrait orientation but the masks are all 90' out so I can't select the 'top' of the image as that mask is show as left and bottom mask shows right. What step have I missed ?

Thanks in advance.

You can rotate the masks as you need. If you can't see the handles, just zoom out a bit. Make sure to not use the internal masks.
You can also rotate the images in Lightroom. After saving metadata LRTimelapse should also show the correct orientation in the previews.