Thanks Jen for your responses.
Here are some more details that hopefully will help locate the problem. I am using an account at http://usegalaxy.org. The problem is independent of my data, as I haven't run any of it through the workflow. The workflow that I am trying to edit is a published workflow called RNAseqTRAPLINE that I imported from the Galaxy website.
In case it was a problem with the server I have started again from scratch today. I re-imported the workflow and used the workflow editor to try and edit the instances of TopHat in RNAseqTRAPLINE, changing from "use a built-in genome" (mm9 in this instance) to "use a genome from history". I then saved. During saving I received the server error "Duplicate workflow outputs with name [out_file1] found", and I clicked on ignore. I then ran the workflow (and was asked if I wanted to leave the page or stay on the page, to which I clicked leave the page). The workflow then appears, but when I click on the steps involving TopHat (e.g. Step 30) it states that it will "use a built-in genome" (mm9), and therefore my edits have not been saved.