Thanks for the replies, these are the results I got. Unfortunately none of them worked, it appears this is a bug. Thanks again for the help and if you think of something else let me know.
That situation could be due to a layer being changed in the top level assembly. This sometimes causes the corresponding layer to be changed in lower level components. Try setting the status of any components in the workspace, which will not be modified, to read only. The only trouble is, for each of these components you will have to hit enter when you save, because of an error message.