Good question, Bill, and awaiting Bryan's reply.

Evidently, the first doubts re 'junk' DNA arose some 50 years ago. In the last decade the doubts have increased:

"Transposable elements (TEs), also known as "jumping genes" or transposons, are sequences of DNA that move (or jump) from one location in the genome to another. Maize geneticist Barbara McClintock discovered TEs in the 1940s... McClintock, however, was among the first researchers to suggest that these mysterious mobile elements of the genome might play some kind of regulatory role, determining which genes are turned on and when this activation takes place (McClintock, 1965)."

"...Moreover, in primates, scientists have identified a SINE known as Alu that seems to play an important role in gene regulation and evolution. These new discoveries are prompting scientists to think twice about dismissing such a large portion of the genome as nothing but 'junk.' "
Leslie Pray, Ph.D. 2008 Nature Education

Now it appears that the 'junk' notion is rejected:

"A staggering batch of over 30 papers published in Nature, Science, and other journals this month, firmly rejects the idea that, apart from the 1% of the human genome that codes for proteins, most of our DNA is "junk" that has accumulated over time like some evolutionary flotsam and jetsam."
Written by Catharine Paddock PhD, Article Date: 09 Sep 2012

"Time is what prevents everything from happening at once" - John Wheeler