The save operations seem to be strange under OS X 10.7 (Lion) and later. Why that?
Under OS X “Lion”, the document handling was deeply revised. PDFactory supports the new features, but they seem to be quite strange under certain circumstances because “Lion” controls some features independently from what the App wants: The well-known “Save” exists in PDFactory only for new documents which have not been saved yet. While working with existing documents, “Lion” saves changes automatically without letting the user initiate this.
But attention: It may happen that documents get saved even though you don’t want it. Thanks to OS X “Lion”. And also the feature “Save as …” was removed and, if offered by the application, is replaced by “Duplicate”.