Fortunately it was very easy (since I had not removed it) to replug the old HDD drive to research the problem.
I looked on the internet and found this article (among many that describe the problem; seems to be something people fall into regularly)
http://www.anotherwindowsblog.com/2011/02/windows-7-not-genuine-after-disk-clone.html
Apparently unless one is excessively careful (as I was by accident when cloning to the SSD for my laptop) windows wil assign incorrect drive letters; inparticular it will not give the system drive the same letter that the BIOS will give it when booting the system. As a result -chaos!
It seems to be necessary to have the new drive in situ and the old drive externally instead of the other way round which is more natural (and that may be an incorrect diagnosis).
However instead of telling you that "something cannot be read " (which is the usual result of an incorrect drive letter and in this case the entire desktop could not be read!) it puts up the "not genuine" message as if it was a pirated copy of Windows.
As desribed in the article from the internet I cited, you have to either install a program from Paragon (who produce excellent software by the way) or manually edit the registry (highly not recommended as it is easy to wreck the system BUT in this case easy enough) to give the windows system partition the drive letter it is expecting.
Once I got up my courage I did that and like magic it worked.
One lesson of course is that when doing this kind of thing (cloning a system onto new hardware, for example) unless you are experienced and competent (and confident!) it is likely to be a lot less hassle to ask a local computer company to do it for you; they have probably already experienced the pitfalls and know what to do to overcome them.