When you add an element that requires a "signal ref" and you save your diagram before typing the signal ref, everything you do from that point won't be saved. You'll only notice it as long as you close and re-open the diagram (or restart Eclipse). So yo could work for hours on your diagram and get everything lost…
I've noticed the issue with SignalBoundaryEvent and at least another element.
Sorry for reporting the issue here but as codehaus is closed is there any other bug tracker ?