The Borrensen web site says the tweeter crosses over at 2.5KHz. That seems too high for the tweeter to generate a whiplash sound by itself. However, my first guess goes with what Erik says -- a woofer bottoming out. That can make a cracking sound, particularly if the recording contains subsonic material. I heard one recording the other day where the musicians were on a wood platform. Everything sounded fine on my second system (no sub) but you could hear them stomping here and there on the main system with a subwoofer. The sub didn't bottom out, but the noise wasn't very musical.
If you have access to DSP or tone controls, it'd be interesting to see if the problem continues if youi back off a bit on the bass, or can cut the response below 30 or 40 Hz.