It's the check everything phase:
How strong (and clear) is the signal coming into the radio? Can you do anything thing to improve this if need be? If there is analog on the same system, how does it sound?
First make sure the audio coming into and also through the soundcard is clean. Can you listen to it "through" the computer? If so, is there a hum on the audio signal? Is the audio cable plugged into the mic or line in jack of the soundcard? If mic, is the "microphone boost" on? A line level input is best, maybe try an external USB soundcard and use the line in.
Have you looked at the signal with a software oscilloscope, like Uniscope? If so can we get a screenshot of that?
The final stage, once you are fairly certain the audio is as good as it gets, it to set the audio levels appropriately. Too high and your soundcards amp will distort and clip.