There is little bug in GNS3 running on Ubuntu Jaunty (9.04). The GNS3 cannot display the workspace which has been configured in *.net file. The GNS3 team said that it is the problem of new vesion of qt library.
To solve the problem, you have to right click on project file *.net and select menu "Open with other application" and browse to gns3 application (If you install through synaptic, it would locate at /usr/bin/gns3) the saved project will show in the workspace.
Thank you to