Firmware 2.65 is definitely the latest firmware. Luckily I don't have any lip sync issues at all so I leave it at 0ms. I have a Roku Ultra, an Oppo 105 and a direct TV box plugged into the 3060.
What you're experiencing doesn't sound right to me. If you haven't called Yamaha, I would recommend it. They have good customer service, they should be able to tell you what's going on.