Ok it looks like I spoke too soon!!
This morning it was working and I completed installation and started work on my new site. This afternoon I go to my site and get this message:
Warning! Domain mapping upgrade for this domain not found. Please log in and go to the Domains Upgrades page of your blog to use this domain.
This login leads to my old Wordpress.com blog, which I thought I deleted.
My new wordpress.org site which was fine this morning now seems to have disappeared. Any ideas what could be going on?