I’ve collected feedback from various users, including Rob-Art over at barefeats.com, and it is clear that the problem occurs with all brands of displays: NEC, Dell, Apple, etc. So it seems that Apple has a nasty bug on their hands. Whether or not Apple will do something about it, and when, is another matter.
The problem seems worst with the Mini DisplayPort and a second display, but since my own situation showed that both the DVI and Mini DisplayPort connectors can be involved, there seem to be no hard and fast rules other than a defective video card that has a determination to annoy.
Since I worked with dual displays for 18 months on my 2009 Mac Pro without trouble (indeed one of them the same display), this screwball behavior clearly falls into the camp of design defect, which we can hope that firmware will address.
On the plus side, I’ve had only a few intermittent black-outs on my 2nd display when both displays were blanked (eg for sleep mode), and those are easily dealt with via the hot corner workaround. But the idea of working with this lemon of a video card (the 5870 or 5770) for the next few years does not appeal to me.
Is this a big deal? Could be for some, but I’m having very little trouble, so I’m not advising anyone to hold off on the new Mac Pro.
Does Apple know about it? No idea, I don’t have the time to spend reporting and diagnosing for them.