i reported this problem some time ago, i guess juan could not get to the bottom of it. IIRC i even uploaded a set of process icons that contained a problem SA instance.
what's going on is that a staralignment process icon you've saved on the desktop is "corrupt". the only way i was able to save my project was to go thru each staralignment process icon, in turn deleting one and then trying to save the project until it succeeded. faced with this the other day, i tried to get fancy and load each process icon into SA and then save a new process icon, hoping it would get fixed, but instead this crashed pixinsight and took several days work with it.
so i would reccomend just deleting saved SA process icons until the project save succeeds, and not double-clicking on any of them.
rob