I've also seen that behavior. In some cases it seems to be a one-time behavior (as in the scenario you described), and in others (e.g., restart), recurring or intermittently recurring. I was troubled by it at first, especially on restart back in 1.0 (which I was doing a lot as I learned how things work), especially since eBox's dialog insisted that I had altered some configuration by hand when I had done no such thing.
Since eBox writes and updates configuration files as it sees fit (which is part of its job), it need not be always clear to the end user what triggers a configuration update and so a "Save." I don't always understand why eBox updates this or that module after I changed the configuration in some other module. Even though I don't know the trigger for this "un-caused" save behavior (and see no reason to know, since I use eBox to reduce my need to know), I don't see it as a deep mystery either. I suspect certain events or series of events cause eBox to clean up or initialize services regardless of user intervention. I do agree that it's disconcerting until it becomes part of the known eBox routine.
That said, maybe one of the developers will provide a better answer and detail the basic mechanics of unsolicited saves.