I seriously doubt it, but it could be the rear end backlash. When test driving my GT, and my father was driving ( it had been 20+ years since he drove stick), the rear end clunked when shifting. When I drove it, the clunking wasn't there.... you just have to know how to drive a manual tranny.
Like I said, I seriously doubt that's your problem. But if you happen to be hearing more of a clunk from the rear diff that a "really loud knock", then it may be the rear gears. All depends on how well you shift.