This seems like a bug and I've logged https://issues.jboss.org/browse/MODE-1617 for it. Btw, creating workspaces does not require a session.save() call, as the operation is considered a "workspace operation".
this error plagued me also. It took me till yesterday till I could pin it down as it happened a bit weirder to me. An way around your problem for the moment would be to create 1 more workspace at runtime than you need, as it seems if you create 1, you get 0, if you create 2 workspaces you get 1 (the first one created), with 3 you get the 2 first created ones and so on....
Hope this is fixed soon,
running fast on ModeShape http://www.whiskyworld.de