I'm not sure the installation is kaput. IT's probably just a case of understanding how workspaces and projects relate.
Note that per your description, the workspace locations are Eclipse and tersus-workspace rather than the .metadata subfolders - if, when switching workspaces, you select a .metadata subfolder, the end result is the creation of another workspace (so that the .metadata folder you selected will itself contain a .metdata folder).
To clear up the mess, I suggest you create a new workspace, and import the projects you are interested in (Guestbook?) using the Existing Projects into Workspace import wizard I mentioned in my previous post. I suggest you also check the Copy projects into workspace check box, otherwise the project will physically remain in the original location and only "linked" to your new workspace.
We do plan to release an updated .deb package, but I cannot commit on a specific date.
For best results, use the Firefox browser..