you did not say what the specific noise was, or what seems to cause it to start...(using a mic input, instrument, midi, pushing record....) OK there are several possible points of entry, or the noise could be happening all the time, with no external audio input connected.
narrow down the source, start with the computer by itself, plug in your headphones, does the computer itself have the noise with nothing else plugged in?
go through each piece of equipment, one at a time, and try to eliminate the possible sources of noise.
Try posting this question in Pro Audio Forum at Tom's Hardware.