How does the Workspace know where to find and how to use the necessary data? If I run from the desktop program my Workspace is looking for four files in four particular locations. How does this translate when using a Workspace in Automator?
Have you upgraded your Automator to 14? Because that is what happened to me when I added a workspace created in version 14 in Automator version 13.5. I tried using a workspace with the same version as my Automator and the paths appeared as I upload it.