I don't know if this will resolve the issue or not, but you may want to try this if you haven't already. Open MicroStation with the workspace you are wanting to use. Then from that MicroStation session, open up Print Organizer and try printing your file. (Although Print Organizer allows different print definitions to use different workspaces, there is currently a problem with that feature that I believe is addressed in the next Select update, i.e. you will be able to have different workspaces associated with different print definitions inside of Print Organizer.)
If this doesn't allow you to get what you want, and nobody else provides a solution, you want want to log a Service Ticket with the Plotting Technical Support Group so additional troubleshooting can be done.
Andrew Edge:Are you running ustation.exe with customized command-line arguments, or using another technique to run MicroStation in a non-standard manner?