I have the exact same sub and I have exactly the same problem as you. It only makes this rattling sound when there is long, deep base tones, but quick bursts, you don't hear it. I think its mechanical in nature and not a digital signal interruption.
Its definitely coming from the inside of the sub. At first I thought it was a break-in issue, maybe the rubber/cobex needs to flex a bit so I put it off from bringing it back, now 3 years later(!), the rattle noise is still there (I don't really use it much anyways but when I do and it rattles, it make for a really crude sounding bass not what you would expect from B&W). My dealer gladly said he would check it out for me and if there is a problem they would send it back and hopefully its not an electrical issue as that warranty has expired for that (5 years for everything else).
Jules, Was your issue resolved? Did you contact B&W and did they identify the problem? If so, what was it?
I also found another forum user who reports the same thing:
hometheaterforum.com/htf/speakers-subwoofers/208092-b-w-asw-600-subwoofer-questions.html
Sorry it took so long for me to update this thread!
anyhow, good news. I tried to contact B & W, and they told me to contact the dealer, as most of their dealers do repair themselves. After I got the run around from the dealer and B & W, i decided to troubleshoot the issue myself. Keep in mind, I'm not familiar with the internal components of the subwoofer. I grabbed an allen wrench so i could remove the driver from the enclosure. I had this feeling in my stomach that the driver may have been loose. Sure enough, the allen screws were very loose, all around the driver. The noise was coming from the plastic surround rattling against the enclosure! I firmly tightened the screws around the driver. It solved the problem

Although, after a few weeks of heavy usage, the rattling is starting to come back. I am considering using some threadlock to solve this issue.
I was extremely happy I didn't waste my time/money getting it "repaired." I just would have never guessed, because i listened so closely to the subwoofer, and could have SWORN it was coming from the driver.
Also, I used a y-adapter to plug in to both of the line inputs, and the output of the subwoofer nearly doubled. Previously, i was using only one, i figured that was okay because that was how my old JBL worked. If you plugged the jbl in with a y-adapter it made no difference.
Hope it's an easy fix for you as well!