ok.. there was one bug in the DataSource step that would cause it not be saved after it has been moved, but that doesn't really explain some of the other errors you are getting.. hmm.. are you seeing any errors in your soapui console window when trying to save you project (when it fails to save..)?
It may have to do with cloning a test case, rearranging the test steps, dragging and dropping, reading Datasource from external files. In my script, I have a combination of all those things. I didn't pay much attention to the console window when I saved a project. But I am sure I didn't see any warnings for the project that I tried to save. Will keep an eye out for the console window next time.
there is definitely an issue when moving DataSource steps (either with keyboard or drag-and-drop) that will corrupt them and cause their changes not to get saved.. but I'm unsure if this could affect all following teststeps (so that they are not saved) and other aspects of the project.. stay tuned..
Anyhow.. we'll try to publish a new snapshot as soon as possible with this one fixed, so you can get some improvement at least!
I think we finally managed to track this down thanks to help from you and other users. the problem occurs when moving a TestCase within a TestSuite (either with keyboard/menu or drag-and-drop), whereafter the internal XML-connection is lost for all testcases in that testsuite.. A snapshot will hopefully be released later today!
thank you for your patience and sorry for the inconvenience!