The device you are referring to is a brake modulator (aka active proportioning valve) that reduces pressure on the rear brakes when the rear of your vehicle lifts up. This helps keep the rear wheels from skidding when the weight shifts from rear to front.
Unfortunately, if you put a lift on your vehicle, the modulator is fooled by the fact that rear always seems to be lifting, so rear brakep ressure is always decreased. It is possible the "clunk in the trunk" is actually your "a-frame" bottoming out if you have a lift. If that is the case, the fix is installing a rear diff correction spacer to lift the a-frame up to the correct angle (as it was before the lift) so it will not bottom out. Correcting the angle of the a-frame will correct the modulator confusion.
Hope this helps,
Gil