After months of this nonsense I think we finally have a solution. We are dumping the $99 Apple adapter entirely and going with a $15 Mini-DisplayPort to DisplayPort cable (
http://www.cpustuff.com/Mini-Displayport-to-Displayport-cable-assembly-2-Meter-p -16240.html). It requires us to buy new 30" displays (Dell 3008FPW) at $1399 each to replace some of our older DVI-only displays, but we have already wasted more than that attempting to help Apple resolve this issue.
I spent tens of hours with tech support and customer relations, but all I ever got was that engineering was working on it. It wasn't until I threatened to return all of the unibody Macs my company has purchased and demand a full refund that anyone at Apple took this seriously. They then FedExed me replacement adapters and called regularly to check if they were working. They weren't, but luckily the cable I mentioned above was just released. Otherwise I was on the verge of placing a 5-figure order with Dell to replace our entire fleet of unibody MB Pros. If Apple refused to take the MB Pros back they would have heard from my attorney.
Apple customer relations offered to pay for the new cables (what a joke, they are $15), but withdrew the offer because they are not sold on the apple.com site. Perhaps they should be.
While they are at it, perhaps they could hire someone who knows how to run a proper hardware/software QA environment. There was clearly no such person involved in the development and release of this adapter.