Mine is also not affected by the electronic systems.
It only occurs in first gear during turns, like at a t intersection, either direction. It is 4 or 5 knocks in the space of a second between about 1800 to 2200 rpm.
It does not really occur in a straight line though may persist momentarilly after the car has straightened.
I live on a steep driveway, and when I pull out of the garage I turn and accelerate up a longsteep hill (1:4 gradient) in first. My vibration has gradually been getting worse, starting from not being a problem at all initially, since I go the car. I suspect this ritual out of the garage is causing the damage.
MY feeling at the moment is that there is a resonance between the Torsen self locking centre diff, and the entire rear suspension sub frame. What follows is total speculation, but I am hoping to stimulate discussion and provide you with some more ammunition for your dealers; but let me explain; (If you are note mechanically minded skip to the bottom)
Firstly, the rear subframe, which houses the rear diff, is mounted to the car on four rubber mounts. These mounts have an amount of elasticity. In fact, I mounted a web cam under the car and recorded the car accelerating. As the prop shaft 'torques up' the rear diff, the reaction torque is transmitted through the sub frame. The sub frame reacts by lifting at the front. From my video it can be seen that the rear sub frame certainly rocks with sufficient amplitude to bottom out on the underside of the fuel tank and cause the thumping noise. I was surprised to see it lifting by what looked like at least 10mm. I think that in my car the contact point is between the subframe housing and the bottom of the fuel tank, immediately above the prop shaft yoke on the rear diff. If you check yours at this point, you may see a witness mark on the protective sheet of metal on the underside of the fuel tank in the propshaft tunnel area.
When I found this my first instinct was to want to replace the vibration mounts on the subframe. I figured that these must be flogged and the subframe is exceeding its design travel. So one day i stopped in at the dealer and looked at a new 159. The mounts looked identical to mine, and had the same clearances etc.. Ive taken out the mounting bolts and from what I can see my mounts are tip-top. This does not rule it out, but has me thinking about what else might be really going on here before rushing in and changing the mounts.
So then I turned to the centre diff. The torsen centre diff, mounted up front in the gear box has a torque splitting function that directs more torque to the end of the car that can take it. If a rear wheel slips, the front axle will see proportionally more torque than the rear axle. Unlike other lsd's, torque is not split as a function of speed. The actual way this is achieved is difficult to get your head around, although it is purely mechanical and involves friction between gears and housings, etc...in the diff. If you want there are some propeller-head explanations linked to torsens website.
OK, here is where I am going way out there. When turning a corner, the front wheels in combination rotate faster than the rear wheels incombination, as they described a larger turning arc. Conversely, when the car accelerates it is easier to torque up the rear subframe than make the front or rear wheels turn. So for a split second the rear axle spins faster than the front axle as it winds up the rear subframe (hence differentiation).
I can't pinpoint it any more than this, but I can see that there is scope for two effects systems to resonate against each other. One is the torque splitting function of the centre diff, and the other is the rear subframe. This cycle repeats itself, hence a resonance.
This means that the centre diff elements are actually meant to be rolling to differentiate the front and rear axles, but the brief wind up of the rear subframe causes one of the elements to momentarilly stop dead, resulting in a stick-slip situation to unbind it. This effect may require a little bit of slip-stick effect in the diff, perhaps as a result of wear to get going.
OR SOMETHING LIKE THAT...
I found some posts on audi forums that had the same symptoms and were blaming the torsen centre diff. Some of those posts suggested that changing the transmission (and therefore centre diff) oil sorted out the problem. I have tried changing the oil in my manual gearbox, and used Castrol Syntrax 75W-90. My first reaction was that it made the noise worse, but I suspect this was just because I was testing it harder during the test drive. I shall give it a 1000k's or so and re-assess.
I also think that it may be usefull to unbolt the rear subframe and temporaily space it down about 5-10mm. Sure this will throw out the wheel alignment temporarilly but it will also increase the clearance to the fuel tank. I have noticed that I can push up on the tank and increase the clearance by 5-10mm, but there is no easy way of holding it there. If the spacers stop the banging, then it may be that the vibration is in fact a characteristic of the car, and that the real problem is that the fuel tank has sagged. That would actually be a nice outcome because its probably easier/cheaper to fix than the centre diff!!