I know Cool Edit pretty well (and they were just bought out by Adobe by the way....now they're called Adobe Audition and it's a little more affordable).

All the suggestions so far are great...I must ask the bone-head question (because it happened to me)

Are you recording your vocals with a mic while Track 1 is playing out of your speakers? That'd do it every time.

When you record vocals you've got to wear headphones and silence everything around you...