As I have said before; I would get the engine problems fixed before spending any time/effort sorting the gearbox problems.
Thanks for a good post bamboo, I think you are right. The VAG support said that whilst it was possible that the ecu problem was causing the dsg to be in 'restricted' mode he'd never seen it happen. But yes I think I should do as you say.
Up and downshifts are both slow. It seems to be taking a long time for the new clutch to engage, and as you say the rest of the gearbox seems to be adjusting to deal with that. When downshifting in manual mode, the car ends up in neutral for a second before slipping the clutch into the new gear exactly as if you were slowing down gently driving a manual.
I keep thinking of things it could be - bad gearbox oil, worn clutches etc, but the fact remains it only started when the ecu was changed, and it's remained consistent every since withouth degrading.
My current theory is that there's a fault in the ECU itself that was not picked up by the suppliers - the short to ground on the flap position sensor is actually inside the ECU - it's certainly not outside it. I've tested the wiring with a continuity tester, one lead clamped to the engine and touching the other on each pin in turn. One is connected to ground, but it's the brown one so it's meant to be.
I tried tackling the suppliers originally, because the part had a 12 month guarantee, but they seriously fobbed me off. They said that the guarantee did not apply because the original fault had not been fixed before the ecu was fitted. This is clearly bullshit because the original fault was not related to this current fault in any way. The other issue is that my contract and hence the guarantee is not with them, it's with the mechanic.