Shouldn't the good condition battery read something like 12.6x Volts ??
12.1V seems a bit to low.
Battery on the S8 had this sort of readings and I was experiencing similar issues so I got new VARTA battery and since then all problems has disappeared.
http://www.ebay.co.uk/itm/Varta-I1-V...YAAOSwojRYSoKQ
Some D3s had issues with the battery management ECU which is in the boot by the wheel arch above the (-) terminal. Can't remember is software update solved was the way to go or just replacing it with a later part number module.
How about changing the last digit of your battery serial number to make ECU think it's a brand new battery in case someone messed around while your car was off road with the gearbox issues for a while?? Unlikely, but worth a go if your battery is still original which means it is kind of due a replacement.
And I say that because on the A8 I've had a good battery, no issue prior or warning light/errors etc and one morning battery has completely died, not even a drop of juice left to do anything and car was driven day before.
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2006 D3 S8 5.2 V10
Ceramic Brakes, Bang&Olufsen, DTV, DAB, Rear Camera, BT, TPMS, Soft Close, Auto Boot, AMI , 4 Zone AC, Home Link, All Electric Blinds, Fingerprint, Ski Hatch, Black Extended Leather, Heated Sport Seats, Alacantra, Carbon Trim inc Aluminium Pack 2.
2015 A3 S line 1.4 TFSI - for the missus to keep her away from my car.
Standard S-line equipment, no extras.
2006 D3 A8 3.7 V8 - SOLD but not forgotten
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