I would try a test then. Something along the lines of;
Take a secondary DAW and output a moderately complex waveform via digital to your main interface. In Nuendo take that signal as your input. Both record and monitor it.
Take the monitored signal from your main interface and duplicate / send via digital to your secondary DAW and record that there.
You should now have three files to compare: Original, original recorded in Nuendo, monitored signal recorded in the secondary DAW from the Nuendo monitor output.
I have neither the time nor the setup handy to do that now. If I find time this weekend and am bored enough maybe I’ll try it.
To me that’s a red flag.
I honestly mean no offense here, but if I got a dollar for every time I’ve read that someone has a lot of skill and experience and can hear a problem and it then turns out there was a procedural problem (i.e. hardware, routing etc.) rather than an actual problem with code - or there never was a problem in the first place which was verified via rigorous testing - I’d never have to work again.
I’ve lost count over how many times I have “heard” things myself that weren’t there. We’re human. We’re biased. Me too, despite also having decades as an engineer and years of being a musician before that.