First question is whether this knocking occurs on all three speakers or just on one of them. Doubt that all three speakers would have the same defect. And does this occur with all music, or just with a particular CD? Also, does it occur using both the digital and analog connections? You need to know all this in order to figure out if it's a speaker issue or something to do with the receiver.

The only sound I've ever heard on my system that sounded like knocking was when my subwoofer bottomed out during a really loud passage. Because your speakers are ported, the only sounds that can bottom out the woofer audibly are the loud ones that go well below the tuned frequency.