Thomas just released a version 6.5 after I mentioned this issue to him on my site. v5 panos work great, but something in versions 6.3 and 6.4 seemed to change the positioning and size of the pano whatever the output settings from pano2qtvr.
Version 6,5 works fine in this respect now, the same as version 5, which I had to use on the FIRST pano rendered on my site. Oddly, if the first pano (v5) was right, they all were OK even if v6 panos. If the first pano was mis-positioned, then they all were even if they were v5 ones! But, as I say, Thomas has sorted it now.
What v6 (including v6.5) appears to do diffeently though is render some hotspots momentarily (for US readers by this word I mean "for a few moments") before the pano appears, and they are out of position, I think because they are rendered without recognition of the fact that I start the pano with a changed pan and tilt (and fov) from what pano2qtvr creates. It MIGHT be my code, but my code works OK for v5 panos, so I think it's rooted in the same issue as Thomas has worked on for the mis-positioning. I haven't been able to find a way to change this. I have a similar issue with the radar indicators on the maps, when I use them. They "momentarily" show the wrong direction and zoom before the pano renders, and then jump to the right place almost immediately. Just a cosmetic, really, but I suppose I'm obsessive...
But this was the same with v56, and so it might be my ineptitude