After the upgrade the slideshow on the homepage of the main site runs fine, the slideshow on the homepage of the weddings site just has loading icon and the slideshow on home of the golf website shows the images at various sizes instead of all the set size -- as it was before the upgrade. The upgrade was a bit of a jump as we hadn't upgraded in a few months. The other galleries are fine on all the sites. I am not using the Flash slideshow at all so think location of imagerotator.swf not an issue.
I disabled the plugin in Network Admin, then realised that the plugin was still enabled on the plugins admin for the main site.
I then removed the plugin completely, but when I re-installed the galleries were no longer recognised by the plugin, even though the directory on the options tabs for all was right.
The images for the main site are in wp-content/gallery.
The images for the other two sites is in /wp-content/blogs.dir/SITE_ID/files.
I tried moving the images for the main site into a blogs.dir/1/files directory which I created, but that didn't help. (I thought there was an import function that I used before but cannot find now.)
I restored the database from before I removed the plugin and I'm back to my original problem with the slideshows on the networked site, but at least I have all the other galleries and images in place.