This isn't a fix, sorry, but a messy work-around, and you'll need to be tech-savvy to make this work for you, but it's working for me, so I'll share, in case it's useful to someone else.
I've set up a VMWare PC image running Windows XP with just the EReader software. I'll never be running Windows update, or installing anything else on this 'machine'
I download the books on it, and then copy them to my real, physical machine which is running Calibre.
It's working fine for me, and I now have a copy of the machine, which I know works which I can revert to if something goes wrong in future.
Hope this helps someone else.