There's a problem with the auto-save service stuff specifically with beta 3. After you stop the service, then restart it - the *next* time you stop it, it doesn't correctly update the service save files, which means the next time you restart it it doesn't load things right. If you manually load the save files, everything will be fine until you stop and restart it again.
We've not found any problem with the actual saving process. It certainly saves all collected data. If you set up any of the targets to ping final hop only, then it would only save that data, but if it's collecting everything, then it should save it too.
Have a closer look at this an let us know what you're seeing. Over the last day or so I've done some pretty in-depth testing of the save system, and it seems to work fine except for the problem mentioned above.