This is what I got from an IPv6-user:
The TLS-handshake succeeds, but after that everything breaks loose. TCP-packets are out-of-order, there are retransmissions. The above packet capture starts at second 23 and there is a failing retransmission at second 53, so obviously there is not much of a service from my website.
There are perfectly working IPv6-users, I have requests from 14 separate IPv6-addresses in log, so it works perfectly for somebody. Ultimately I have no idea what's going on, or how to fix it. If you know, drop me a comment.
I got a disc failure. Luckily the server has a RAID, so no imminent data loss occurred. However, it is a RAID-5 setup, so the system performance was impacted heavily.
Now I transferred the entire system into Microsoft Azure and it seems to be running little bit better. The project was a huge one and I had to tinker with it a lot. I guess I'll have to do a full discosure about that later.
Hopefully this thing stays working this time.