This is fairly commpn in mixed setups. and is also evident in HU's with volume levels being different between FM and the CD player. Better HU's have controls to balance levels. In a Car PC setup yo have to do it manually. Bring the low levels up as high as you can without distrotion. using the PC mixer volume controls. Drop the volume on the analog side using a EQ line driver or attenuator. Then control overall volume via the DAC and the amps. DSP in cars is a balancing and setup chore as posted previously in another thread. But once set up the quality improvement and noise rejection is well worth it.