The people with mechatronic issues had flashing symbols, but I believe it can also be for over-heating (something I think I read but cant be sure where) was it just the D that flashed or all the symbols? Hopefully Vagcom will have the answer.
might be worth reading this wiki article http://en.wikipedia.org/wiki/Direct-Shift_Gearbox has some interesting insights into the box, and I was suprised by the statement of moving it into N if stationary for a long time, I have always been a leave it in D with the brake fully depressed, as assumed it was fully disenaged clutch with 1st ready not sat on the bite point.
Those with paddles may also find the stopping it kicking down line interesting, havent been able to test yet since only driven round town.
You should treat it as a normal gearbox, in regards to short stops, if it is only going to be a quick stop then you would leave it in drive, just like in a stick shift, if you are going to stop for a very short period, you would just come out of gear and place it in first.
And the same applies when waitng at lights, again stick shift you take it out of gear and release your clutch, same applies to the DSG.
Whenever i get the opportunity i select Neutral, after all it's only a quick flick of the arm.
I cant remember the exact explanation That TT gave but leaving it in D - mode, at say a set of lights, heats the oil up at its quickest, something to do with it's positioning in the box.
Also i dont know were you got the info about people with the mechatronic unit problems had a flashing light, in my own experience and the ones i know about, there was no flashing lights.