Stud. Theol.,
Sorry to hear about your progress so far this year regarding applications. I didn't get into any programs last year and was kinda bummed, despite having 2 M.A.'s, a 4.0 GPA on my last one, great GRE scores, adjunct teaching experience, and great recommendations.
I can relate to a lot of what you said. My M.A.'s are in precisely the two fields you mentioned: analytic philosophy and Christian systematic theology. Finding a PhD program that allows one to combine both is a challenge, but I do think there are options.
I'm surprised you said that the faculty you spoke with at Boston University didn't seem helpful. Did you speak with Dr. Garth Green? Besides being a genius, his research and teaching interests are right at the connection between philosophy and theology (http://www.bu.edu/religion/faculty/bios/green.html). I spoke with him about a similar project for doctoral work, and he was quite helpful and informative. There were some others at BU who also seem to have interests up that alley. I got into Boston University this time around, and am quite excited at the prospect of studying there. Also, they have the Institute for Philosophy and Religion, which I think would also be helpful.
Regarding Chicago, I've also applied there and am waiting to hear word from them. I spoke with Gamwell, and he seemed understanding of my interests. Chicago might be more difficult for one from a more conservative theological background (from what I've heard), but it still might be possible to engage in a project of that nature if one were willing to broaden it a bit.
You may want to consider another program that i'm waiting on: Marquette's Theology program. They have a program called Theology and Society which is specifically geared toward interdisciplinary work, and they are very open to integrating philosophy with theology. As a matter of fact, they consider a solid philosophy background as being crucial to doing good theology, and advised that I stress that on my application. Dr. Stephen Long does a lot of work on Barth and also is very much engaged in philosophical theology. Mark Johnson and Ralph Del Colle would also be great for such projects.
Hope that helps!