I've tried a couple of iterations of trying to save simulation files. I find that if I open up Universe Sandbox and start a new simulation or open up a saved simulation, and I simply attempt to save a file, it saves correctly (even after running for a length of time). However, as soon as I check the 'Use multiple processors' option, Universe Sandbox will no longer save files. The program looks like it's saving (wait icon shows up and then disappears just as it would when saving), but when I look for the save file, there is no save file. I've also tried saving the file as the default save names (i.e. My System - 20120710-174216) or even something simpler, such as (save test), and still no save file.
Again, the save function works correctly until I check the 'use multiple processors' option. After it's checked, although the simulation runs faster, it will not save from that point on.