Any disagreement involving BL and proponents of ID, Henry, tends to reduce to two bottom line issues, although other matters can also come into play, depending on the views of the specific individuals in a given exchange.
(1) Is “design” a strictly scientific inference, or does it go “beyond science” into metaphysics and theology? ID folks say that it’s mainly scientific, and leave the metaphysics for later–or for others. BL folks think the design inference is inherently metaphysical and/or theological, even though scientific evidence is involved in drawing the inference. In other words, contrary to what is often alleged, BL folks do believe that certain scientific evidence points to “design,” but we unabashedly think that the “designer” is a supernatural God–basically, if the entire universe has been “designed,” a supernatural God is the only viable candidate for that job–and we typically draw such inferences mainly (not exclusively) from cosmology and philosophy, not from biology.
(2) In most cases (Behe is an outstanding exception, and so is Michael Denton), proponents of ID very strongly oppose common ancestry, whereas BL folks do not. For a pertinent recent example, see the book by Ann Gauger and others discussed here: http://biologos.org/blogs/ted-davis-reading-the-book-of-nature/science-and-the-bible-intelligent-design-part-5. Even though this opposition to common ancestry isn’t written into the core of the ID position, in practice it means that ID often collapses into a type of OEC position, with the biblical issues being deliberately buried beneath the surface in order to avoid bringing “religion” into the science classroom. Basically, on this score, ID proponents want to ensure their audiences that the evidence for “macroevolution” is sketchy at best, whereas at BL that’s not on the agenda.