I dont know what software program your using or if your using an external mixer. I use Sonar XL with a Tascam mixer. I was getting that myself and had a little fun using this anomoly as a cheap but decent sounding reverb by using the track volume control to control the feedback from the other tracks. Anyways, by opening the recording option in Windows Mixer> deselecting "What you Hear" > selecting "line in". In Sonar I`d turn off "input monitoring" and take the volume control of the track down to 0. When I arm the track the level in the track is controlled by my mixer, or vol kobs on guitar, I just leave mine wide open all the time on my bass. I get no ghosts from the other tracks.
NOTE: If you're recording in an altered state of consciousness don`t forget to turn the volume of the track back up AFTER tracking so you can hear it, or you'll be checking wires and retracking and then changing out the sound card to see if thats the problem as well.