Why has this happened? Perhaps it’s because Behe was embarrassed by the evidence presented in the Dover trial by folk like Dr. Miller, who memorably demonstrated how Behe's favorite alleged example of IC (the bacterial flagellum) could've evolved from different arrangements of protein with different functions. Perhaps it was because, under oath, Behe was presented with a large pile of publications that covered the general topic of molecular evolution, literature that "Darwin's Black Box" attempted to suggest did not exist.
Or, more poignantly, perhaps it is because there is something like a revolution underway in comparative genomics which is providing, as Sean Carroll has phrased it, forensic evidence for molecular evolution. Here’s a particularly good example of the kind of thing that gives Michael Behe and the rest of the folks hollering ‘irreducible complexity’ fits: a highly-detailed and through account of the putative evolutionary relationships of a particular family of proteins, the globins.
The study in question ("A phylogenomic profile of globins", by Vinograd, et. al,) appears on-line and compares 330 different prokaryote and eukaryote genomes. The massive bibliography takes up nearly eight full pages and contains 147 citations. At the end of the study, there are several graphic displays of the data relationships, including a very neat and easy-to-follow Venn diagram on page 31. The broadest conclusion of the study is that there is a clear pattern of molecular evolution within this family of proteins, which in the prokaryotic genomes are neither as widely-distributed nor share the same functions as in eukaryotes. More specifically, the results support the claim that (quoting from page 3) "since the hemoglobins in organisms other than animals are enzymes or sensors, it is likely that the evolution of an oxygen transport function accompanied the emergence of multicellular animals."
Kitzmiller v. Dover Area School District. Trial transcript: Day 12 (October 19), PM Session, Pt. 1 URL: http://www.talkorigins.org/faqs/dover/day12pm.html