The background: I have a project that I last built on 10.5 on a PPC computer using xcode v3.1. It builds against the 10.4 SDK. I now have a MacBook with 10.6 on it and Xcode v3.
I had the same issue on iPhone, when building a projet that linked against custom static libraries. I seems XCode complains because it can't find debug infos for some of the linked objects.
I fixed the problem by disabling "Perfom Single-Object Prelink" in the library build settings.
I don't know how well this solution applies to the initial issue, but as this page is the first Google answer…