Despite what people think, they’re constantly changing/improving the audio engine. Download SX3 and you’ll hear an even more dramatic change. It’s a more subtle change each major release. Jump back 10 or 20 years and it become super obvious to anyone who has decent monitors and converters. Usually it’s a change for the better. However, whatever they did in Nuendo 4 was interesting and I wish I could select the Nuendo 4 audio engine in Cubase to mix on every now and then.
I’m not surprised you will notice a difference from Cubase 6. It’s about 10 years old and there are even documented changes to the mix engine since then. New mix engine has been a feature in a few versions of Cubase since version 6. It’s not a secret.
I don’t know if it’s the mix engine or just how it communicates with the asio drivers or whatever but over the years they’ve gone from 16 to 24 to 32 to 64 bit so obviously there is going to be a difference. Generally speaking, you get more detail in each release of the audio engine but sometimes it would be nice to hear the old mix engine. People will try to disprove this by bouncing out audio from each version and phase reversing it. Sure they bounce out the same but that doesn’t mean what you’re hearing is the same. Put a highly detailed mic in front of your speakers and record the same session in across different versions of Cubase and I can guarantee they won’t phase reverse each other out. I might do it for a YouTube video in the future.
Anyway, yes they are different. It might take a little while to get used to but technically speaking, it has more information so if your song sounds worse, it’s just more stuff you need to fix.