Sounds like it could just be a LEVELS issue.
Volume level has a marked effect how audio “sounds,” quality-wise.
Make sure as you monitor FCP, that the levels (not the controls, but how loud it sounds in the room) are the same as from the other sources.
If there is still a difference, post again.
BTW, under the User Preferences (FCP pull-down menu)
How many Real-time Audio Mixing tracks are your pre-sets for?
Is the Audio Playback Quality set to “High?”