I thought I'd try posting one more guess about the system killer so you can all enjoy my wrongness one more time
So here it is: there wasn't just 'more than one' system killer, there were a lot of them, as in thousands at the bare minimum. The reason why I'm guessing that is because, as we know, there is one of them still operating five billion years after they were built and deployed, and that's amazing. Of course the system killer's creators would have undoubtedly built it to withstand anything the battlefield and interstellar travel had to throw at it, but surviving five billion years is a very different, and much more difficult, technical challenge. More importantly it's not a technical challenge its designers would have thought about, after all it's still going not because they wanted it to still be running after all this time, but because they just didn't care what happened after it had anihilated "the enemy". What's more, the obvious first steps in making something that might endure for five billion years (adaptation, self replication), would be things that might allow the enemy to subvert the system killer, and hence would have been discarded as weaknesses.
On that basis it seems likely that Sparky has survived the long eons since his creation primarily by luck. That means that for every system killer still roaming around wrecking the universe, there are a lot of them that didn't make it. Five billion years is a long time, and the universe is a very big place full of very dangerous things both naturally occuring and otherwise. In the end it doesn't matter how big and bad you are, I'd guess the odds are very much against any single
machine surviving that long.
That said, it's still quite possible that Sparky was unique when he was created, but the mindset behind his creation doesn't seem to be that unusual, which could mean that a lot of civilizations have ended by deploying a doomsday machine like Sparky. As I said, the universe is a very big place, with plenty of room for a large number of civilizations building many terrible things. Of that profusion of ancient monsters, Sparky might not be unusual in power or intent, he's simply the only one lucky enough to survive.
There is however a third option which did occur to me, although it would require quite a few things to be true as Obi-Wan said "from a certain point of view", so I wouldn't take it too seriously
. Tinfoil hats should be worn beyond this point
: Sparky didn't survive, at least the original didn't, Sparky died a long time ago, but not before the Von Neumans, or something like them, weighed, measured, and possibly ate him. They filed the design away so that they'd have an efficient solution to certain 'problems' if and when they emerged. Whenever they decide that its time to resurrect Sparky again they don't put him back together quite the same as he was, after all they have quite different problems for him to work on, and that needs a shiny new Von Neuman control system where Sparky's brain used to be. Most of the time that's enough to keep him on a leash, but the trouble is that the system killer was built to prevent any attempt to subvert its mission, and every now and then some well hidden security system that the VNs have never been able to completely eliminate, wakes up in the belly of the beast, it removes the invasive machinery, repairs the 'malfunction', and suddenly Sparky's back. Of course this is pretty serious tinfoil hat territory, since it would mean that Sparky only the last survivor of his war because someone chose to resurrect him (which requires a specialised definition of the term 'survivor'), and that VN warships are not system killers, in the same way that a dog is not a wolf, if dogs sometimes spontaneously reverted to being wolves for no readily apparent reason.
You can remove your tinfoil hats now, and return to sanity, where I am almost certainly wrong