I had this same problem, using an old version of the route-me library. I "skipped" all the libraries, and the libraries inside of libraries (proj4), but I still had the same problem. Turns out that route-me and proj4 were installing public header files, even when the libraries were being skipped, which was messing it up in the same way! So I just went into the route-me and proj4 targets "Build Phases" tab, opened "Copy Headers", opened "Public", and dragged those headers from "Public" into "Project". Now they don't get installed in $(BUILD)/usr/local/include, and I'm able to make an ipa file from the archive!
I hope Apple fixes this horrible usability problem with XCode. It gives absolutely no indication of what's wrong, it just doesn't work. I hate dimmed out controls that don't tell you anything about why they're dimmed out. How about instead of ignoring clicks, the disabled controls could pop up a message telling you why the hell they're disabled when you click on them in frustration?