So it looks like bad temperature sensors are causing the issues in the side vents. The driver's side always reads 6* and the passenger's can read between 5 and 47! I bet those are going to be fun to change...
The centre vent is a bit more of a mystery - the potentiometer is working as I can see it in VCDS, and I can even hear the motor moving in response, yet it still blows ice cold under all conditions. Oddly my '99 did that too.
Also a mystery is why the centre rear vents always blow varying degrees of warm, even with the temp set to Lo. Everything up front is ice cold then, and the heater valves are off, yet these vents are still no less than ambient.
Basic settings worked fine, and all the learned values are plausible so I'm slightly puzzled. More vexing is that we're going on holiday tomorrow and are going to have to take the A4 so the family doesn't bake in the back
Edit - more digging shows the temperature sensors are in the centre housing and looks like they're quite down low so what's the betting they've been drowned at some point? One sensor per-side may well explain the centre rear vents as well, but still not the front centre one.
Edit edit - even more digging reveals that the centre vent is actually controlled by two flaps - one after the evaporator, and one after the heat exchangers. Blending these enables it to be controlled independently of the rest of the vents, although the hottest it will ever get is as hot as the rest of the system, so if the heater valves are off the centre is going to be cold regardless. Leaving the control on hot should mean it tracks the same temperature as all the other vents, but can be cold while the others are warm. It appears that it can't be hot if all the others are cold though. The user manual doesn't refer to this behaviour at all. It seems like mine has the cold flap working but not the hot one so a specific output test is needed on V68.