Yes, "The Practice" is Fox also. As is "Ally McBeal," "Picket Fences," etc. I'm not sure if Kelley's ever done any TV that wasn't distributed through Fox.
I'm inclined to think that maybe music rights are hanging up the release of at least some of his shows. Certainly "Ally" used a lot of licensed music throughout the series. Others may not have used as *much* as "Ally" did, but I seem to remember music figuring pretty significantly in most of his recent shows in one way or another.
The DVD for Boston Legal was put out by FOX, the show just airs on ABC. The studio that produces a show is responsible for the DVD set not the network that airs it. For instance My Name is Earl, airs on NBC, put on DVD by FOX. House, airs on FOX put out on DVD by Universal (NBC). When you watch the end of the show when it airs, it shows the studio that produces it.