I would check to see that the speaker tinsel leads are not slapping against the back of the sub. This sometimes happens and can cause a rattling at louder volumes. If this is the case, you might be able to move the tinsel leads out of the way or protect them with some foam.
There are a few other issues that could cause the rattling, but you need to examine the sub. Perhaps the voice coil has come partially or totally unglued from the sub. Maybe the suspension has ripped and is not keeping the voice coil straight in the gap.
Also, before pulling the sub, check to be sure the sub was actually secured to the box sufficiently.