We have lots of sites running, some of them in multi-site and some of them as stand alone sites. Some of the multi-sites are in folders and others have mapped domains.
We think that the affected sites have two plugins in common:
Google Analytics for WordPress - Joost De Valk
Google XML Sitemaps with Multisite support - Mario Kostelac
I've tried deactivating both plugins, but we still get the same problem.
We can add an image url in the pop up media files window, update it and when it's opened again it disappears.
Very unusual and strange that it's affected so many sites all of which have different set ups. As you say there must be something that has changed, we just don't know what and it's certainly nothing that we have done manually as some of the sites are single installs and have not been worked on this week.
We have not upgraded either of the two plugins listed above.
Thanks for your thoughts, if you have any other suggestions, feel free!