I have exactly the same problem. My V6 box is connected to the Hub 3 by Ethernet cable and to the amp by HDMI cable. All channels, Netflix app and YouTube app audio synch fine. It is only Amazon Prime that has the problem and it is intermittent. For example, I watched two episodes of Justified back to back last night. The first synced fine, the second had a massive lag.
i don’t think that the amp processing the sound is to blame for the audio lag, as it would happen all the time. Like Mick, I get perfect sound with live TV, recorded TV, via Netflix app and via YouTube app, either stereo and 5:1 depending on the broadcast - and sometimes with the Amazon Prime app, but not always. On Wednesday night I watched several programmes on Amazon Prime with no problem, yet a few days earlier the audio lag was very evident.
Could the processing speed of the V6 box be to blame? It did occur to me that on Wednesday I wasn’t recording anything whilst I used the Amazon Prime App and had no audio lag. But when I did get audio lag earlier in the week, I think I was recording programmes in HD.