A lot of us have experienced noise from onboard audio when in a vehicle environment. It'll sound clear as a bell on the bench and then you hear all sorts of whirs & pops & clicks that echo activity from PC components (especially disk seeks & mouse movements). This tends to happen due to minor ground loops. To help you can:
- ground everything to a common point
- use a 'ground loop isolator' (insert Marvin the Martian imitation)
- use a USB sound card
I hope this helps.