What’s happening inside the UltraRendu is radically different when you play a FLAC via UPnP vs playing via RAAT – RAAT streams the PCM, so no FLAC decode is done… this FLAC decode in the UPnP case is very slightly adding CPU usage to the stream processing. That might be causing unintended effects to the analog processing stages later down the audio path.
With the right equipment, you should be able to tap the USB output of the UltraRendu and capture the stream of USB Audio data – I’m sure it’s the same. What won’t be the same is the EMI/RFI – but it shouldn’t make a real difference.
If you really want to know if you are not having a error via bias, try getting someone to help you to do a blind test.