UPDATE:
I've done some further testing and I think I have found the bug. I think the above it probably not the issue.
It appears that if there is a variant with only one option to choose from; for example a drop down with only one colour in it then the SKU fails.
i.e. you get the SKU for the main product in the order but NOT the SKU of the variant group.
If I add another variant to the "colour" drop down and update the variant group then it works fine.
There seems to be a bug in the way the module handles drop down controls with single items in them.
Can you investigate please?
We are using the latest version from trials.
thanks
Angus