In my experience, overspeed are generally caused by stupidity or a mechanical fuel control failure, usually a nut or bolts that falls off. I've made it a point to myself on smaller machines to do a careful once over of the machine's governor mounts, linkages, wiring etc, as part of the oil change routine - 250-350 hrs. I have not experienced electronic failures causing overspeeds, although I am a fan of the idea of having a mechanical overspeed system on all engines - hopefully it is simple to operate, allowing for routine, worry free testing.
My most recent experience with overspeed, resulting in a 150 kW generator overspeeding, damaging the alternator, was the result of a lack of proper equipment, and subsequent lack of training to work around first issue. The engineer on duty was using what was shown to him to be the normal way to shut down a detroit diesel, which was by overpowering the governor linkage to shut down fuel. In a rush to do something else, things, of course, went awry, and he increased fuel. The funny thing with overspeeds, it does not take long to create damage. This incident was compounded by a lack of overspeed protection.
The generators now have overspeed protection, but more importantly, have a simple electro-mechanical way of shutting down - on off switch, hopefully preventing human meddling with the mechanical fuel control mechanism.
I hear new ships will run with one engineer and one dog. The engineer to feed the dog, and the dog to make sure the engineer doesn't touch anything.
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Martin's Marine Engineering Page