Was the second hand one known 'working' or just from a wrecker/online ? You'd be unlucky but you could have ended up with 2 'bad' ones... consider this: the alignment process actually started all my issues - my car was running okay before I stupidly did that. Vagcom was fairly new to me at the time and I was experimenting with all the great things I could do When contacted afterwards, Vagcom assured me the process was safe, and indeed the alignment worked fine on my new TB, but there's no doubt that performing it on my old TB caused or at least triggered my issues - probably the most likely explanation is that there was an underlying age related issue there, but while the thing was in the correct alignment it wasn't manifesting itself. Try to align it and you end up moving/clearing the TB out of 'correct' alignment and then due to whatever issue not being able to realign it properly.

I guess what I'm trying to say is even if the second-hand TB was working in whatever car it came off, the first thing you do when fitting it to yours in an alignment and then if they do have a common failure/weakness (which they seem to) it's not unlikely you end up with another failed unit on your hands.... the fault could be quite common with the old units but most people would never know as they don't go around trying to align them If you're getting parts from wreckers I'd take vagcom, plug the TB in at the wrecker and make sure it aligns before accepting the part...I can't 100% remember but I don't think it needs to be physically bolted to the manifold to do this does it? - that's all assuming your car is still driveable on the old TB of course...