After two days of intensive search, the cause of the error reported by ScottG has been identified: non standard file names.
Volume, folder or file names with space —e.g. My first project.ino— , number as first character —e.g. 3D_library.h—, special letters as . + ~ —e.g. Wtv020sd16p.cpp~—, among other cases, raise an error with GCC and make.
This is not specific to embedXcode.
I've updated embedXcode to deal with those cases and plan to release it soon, but I strongly recommend to avoid the cases mentioned above.
Needless to say I can't provide support for issues which are not related with embedXcode, as two major challenges are ahead: OS X Mavericks with Xcode 5 and Arduino 1.5 framework.