I don't know what sound card your using, but if it's a SB try this.
Right click your speaker icon in your tray.
Click on "Open Volume Controls".
The "PLay Controls" control box appears.
Click "Options", then "Properties".
Go to the "Adjust Volume For" and click the "Recording" radio button. Then "OK".
Another "Play Controls" box appears, except this one is called,
"Record Controls".
Look and see if the box is checked on the "What You Hear". If it is, that's your problem. Uncheck the box.
You'll want the "LIne In" box checked. Or what ever box your using to feed your soundcard.
When the "What You Hear" box is checked it'll record everything that goes through the soundcard, your other tracks, the metronome, etc.
While your threre, check your panning, (balance) controls. Center them if they are not already.
Hope that helps.