Your newest blog entry is a godsend! I also have the Magura Marta SL (the same as in the pictures) and while braking power et al. is generally fantastic I constantly experience problems with the pads not properly self-adjusting the way they should, interestingly this only happens with my rear brake and I have never had problems with my front brake. According to the Magura website the solution is to "mobilise" the brake pads, which I did to the best of my knowledge but to no avail...He hits it right on the head. These brakes feel AWESOME when they're working right (heck, I have them on two bikes), but they're finickier than a vegan in cheese shop. There's something about German engineers that makes it impossible for them to make anything simple (or work right unless it's made out of machined aluminum and steel or carbon fiber). I have a Volkswagen, for example. I LOVE driving it. It handles extremely well and the engine is totally reliable, but the radio keeps breaking, the ashtrays have fallen out and the handle on the glovebox broke off. It has had 5 recalls, four of which were for little plastic bits, and if you don't use the best synthetic oil and best filters, changing the oil meticulously every 3,000mi, it will grind to a halt. BMW is also notorious for electrical problems and being overly complicated. Tune, maker of all bicycle things beautiful in metal and carbon, has mind blowingly awesome stuff, (provided you sell enough organs to afford it) but it's all wonderfully fiddly too, as only an engineer can appreciate...
Back to the brakes (note: this is relevant to most open system disc brakes, not just Magura). Under normal conditions, the seal around the piston in the caliper is designed to flex a precise amount when you squeeze the brakes (see pic). When you release the brakes, the seal flexes back, leaving the pads a precise distance from the rotor. As your pads wear, the piston slides through the seals because it has to travel farther than they can flex, readjusting the pads every time you brake.
As the pads wear down and the piston moves outward, more and more fluid is pulled out of the reservoir to fill the extra space. This would be all well and good except that to keep air out of the system, the reservoir is sealed with a flexible membrane (see photo). When fluid is pulled out of the reservoir, the membrane is pulled inward. As it tries to spring back to its original shape, it pulls back on the fluid, trying to bring it back into the reservoir. Most of the time there's no problem because the piston is seated firmly enough to keep the membrane from pulling fluid, but when the pads get very worn and the reservoir is nearly sucked dry, I have found there is enough suction to pull the piston back.
My assessment of the problem, using ESP since I haven't seen your bike, is that you drag the back brake a fair bit (most of us do), and the pads are quite worn, resulting in the phenomenon above. The solution is to top off the reservoir as described in the third trick in the last post including step 5.
Edit: also make sure you're not leaking fluid (check to see if it's wet inside your lever). The Marta SL had a serious leaking problem for a while. If you have a leak, call magura (it's the one in Olney, Il) and they'll make it right.