The problem has been resolved, but I'm not sure why it occurred in the first place or how this resolves problem technically.
When we installed the new version, we installed it once for development, licensed it and then copied the whole directory to a runtime version, and re-licensed that version so that we could run our application. When the copy was done, we had not preserved the properties of the files and so the symbolically linked files were brought over as copies of the files they were linked to, rather than links. To me, that should have worked as well as the symbolic links, but for some reason it did not. I copied the directory again, this time preserving all properties of the files and now the problem has been cleared up.
I think our new M.O. for installing the runtime version will be to re-run the installation script a second time rather than copying directories around :) .
Thanks,
Michael Laporte