Crygil has the official word: Blizzard has completed their updates to the servers, and they are now saying performance is much better: all realms have "shown an improvement in instance performance as well as a noticeable reduction in the amount of players hitting the instance limit." Note that they don't say the issues have been solved (no one would say that everything was fixed, because it never is), but there should be a marked improvements in the "additional instances" bug. In the immortal words of the great Douglas Adams, "We have normality. I repeat, we have normality. Anything you still can't cope with is therefore your own problem."
And we're sure lots of players will welcome this news. At least until Cataclysm, when the flood of rerollers and werewolf fanatics taking on all of the new content and areas in the old world brings the servers back to their knees once again. But until then, enjoy your runs.