I primarily stream using a Marantz ND6008 or use a turntable (pro-ject classic) so I can't talk to the USB cable.
You will find the LS50's will reproduce your music true to how it was recorded. I have some Jefferson Airplane albums where Paul Kantner & Jorma Kaukonen's guitars seem to have a distorted hiss that causes listener fatigue. Where as, listening to say a well recorded Steely Dan album sounds fantastic. I have added a Kef 12b sub to my mix and used a cross over point of 100 to relieve the LS50's from working hard to produce the lower end. The sound is very nice.
But with all that said, the LS50's will tend to reveal everything about the recording, they are considered a "monitor" type speaker. They will mellow a bit over time, but they are very true to reproduce the recording quality of the music and that's both good and bad as you are finding out. Try listening to some artists that are known for demanding high quality sound, one example might be the Grateful Dead's American Beauty or Workingman's Dead, or Traffic's Low Spark of High Heeled Boys.
In the end, the LS50's reproduce a fairly accurate and open sound, that's how they were designed. I have them matched with a Parasound P6 and A23+, both of which are known t have a clear and true sound (maybe considered a bit cold).
The other thing to consider is the size of your room. The LS50's use a 5 1/2" driver and will begin to distort if pushed to hard. They ideal for smaller rooms (mine is 10'x20x10) but may struggle at reproducing reference volumes for larger rooms.
If you are using room correction software, I would try turning it off and try direct/flat. The LS50's are really designed to be true to the recording and not color it (warm or cold). I am not sure what amp you are using but it should be a decent quality amp of at least 50 watts although the LS50's will enjoy more power too.