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I'm pretty sure all the HC3s have some check for genuine Sony batteries. My HC1 which pre-dates the first HC3 models checks for genuine Sony batteries as well.
What has happened is the generic battery manufacturers had figured out how to fool the camcorders... so when it checks for a genuine battery, the battery appears to the camcorder to be genuine even though it isn't. This is why some generic batteries work and some do not.
To make it more confusing, I believe the later HC3 models added some extra logic to do a more detailed check - so now some batteries which may have worked on earlier HC3 models no longer work. But I assume the generic battery makers are fighting back and enhancing the batteries so they will be accepted by the newer HC3s...
The net result of all of this is if you buy a generic battery it may or may not work on your HC3, even if it works for other HC3 users. Make sure you can return the battery easily if it doesn't work.
It's an extra hassle risking that you may have to send it back, but one worth taking IMO. It's criminal that Sony spend time and money changing their product so that they can rip us off with expensive batteries, and I'll do what I can to get around it.