I don't know about Audi's specifically, but many newer computer controlled automatics "learn" the way they get driven. If you always drive with your foot to the floor when passing people, the ECU will get in the habit of ramping up line pressure and holding your shift points longer when you are at WOT for example. It's also why weird things like a faulty mass air meter can make the transmission act up - the engine may not have a lot of load on it, but the signal the ECU is getting from the faulty meter is confusing it, so it won't apply the correct line pressure, shift points, etc for the given engine load/RPM. My genius tech friend explained it to me much better than that, but that's the "I drive a '90 Civic 5 speed" technical version of it. When he services a transmission in a vehicle that has had a hard life trying to get it to smarten up, after the fluid/filter change etc, he will disconnect the battery for a few minutes, then take the vehicle for a long test drive, taking it easy. The ECU has been reset by the battery disconnect, and for the first while of the test drive it's "learning" to shift/act normally again.
If driving your car "normally" seems to result in the transmission not acting up, it seems to me that the transmission had originally learned to operate normally, and perhaps your hypermiling techniques were confusing it? The same way a faulty sensor would cause it to act up, the ECU is looking for one set of learned parameters and is stumped with what it is actually receiving. For what it's worth, it's free to disconnect the battery, try it and then just take the car for a normal drive, see if it does anything weird. My advice is free so take it for what it's worth ha ha, good luck.
Edit: Adaptive transmissions, that's what they are called, now I remember. Here's some idea of what I was getting at
http://www.thetruthaboutcars.com/200...transmissions/