OK, for the benefit of anyone else this happens to...
Take a backup of the database (why not)
Uninstall and delete the files for the plugin
Re-install the plugin
You should find that the user groups that you set up are still there, except they have lost all their settings (which was what you had before after the upgrade).
However now you have re-installed you should be able to set the users to their groups and the pages to their groups, test a couple to make sure - the pages and users now hold their settings after you save.
Once you have done that, you are back in business!
(Alex: if this happens again with an upgrade and it can't be avoided then it is a bit of a fright that everyone can access everything - it would be better if you could set something so no-one can access anything)