Another issue may be that your bumpstops are moving.
Wait, you need to hear why before you slam this.

The Eibach kit said to trim the bumpstops. However, when this is done the rear bumpstop on the accord gen 6 will bounce up an down. My shop made some compression fittings to keep my bumpstops from bouncing up and down as the rears are hollow unlike the front, and they will fall down the shock shaft. Jschmiddy's shop likely did the same to his in the rear[h&r's]. In any case I drive hard and have never had any noise from the rear of my car. My Eibachs have been in and out twice so far to install koni's and the springs are still golden.

Again my buddies 2000 Lude had worn rear shock bushings that caused a clunk that sounded like the muffler hitting something. Again it turned out to be worn shock bushings it happened worse in the winter. This noise appeared around 29k mi and he had them replaced under warranty, problem solved but the dealer said it would return eventually, perhaps your bushings were man handled too much during your install and they need to be replaced? Perhaps your factory shocks are wornout aswell and need replaced.

Your prokits should have also had a rubber sleeve that fit around were spings hit on coil bind. The directions state to postion these sleeves as the stock ones were placed, was this done aswell? BTW-stock springs are progressive too--they coil bind as well that is why they have rubber sleeve too. Again, 3 years, 40k mi of hard use and my Eibach prokits perform with out complaint, I would seriously second guess your install, your directions may have also called for the transplanting of the OEM rubber sleeves to the prokits. This had to be done with springs out of the car.