This sounds to me like a software problem rather than a hardware problem. I doubt it has anything whatsoever to do with it being a dual shock controller. I expect that some entry has been scrambled in your PS3 with regards to Bluetooth registrations. So I'd concentrate on that.
That you've swapped controllers and the problem persisted implies that the bad entry isn't actually for the controller being affected, but rather for one of your other controllers. As if the code were going down the list of registered controllers, and some bad entry kills it. Any controller added after that bad entry can't work.
I'd try turning off the PS3, hitting the reset on every controller you have, and then re-syncing each controller via the USB cable with the troubled controller re-synced last.
Have you had friends over with their controllers? It might be associated with a controller not currently in your possession.
Other than that, there's a recovery menu that you invoke by holding down the power button while you turn on your PS3. Something like rebuilding the database might resolve it. Careful though, some of the recovery options lose things off of the PS3.
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