I just installed the latest version (rev 59 I think) of EmbedXcode and I'm having a couple issues. I created a new project. I did not add any code yet. I noticed my .ino file was still listed as txt, not C. I ran build and I got an error on my Dallas library. So I set USER_LIBS_LIST = 0 and tried again. It said the build succeeded, but then it said it could not load my project because of workspace integrity. I closed xcode and tried again to open the project, but it didn't work. I deleted the bad project and tried it again creating a new project and I had the same result.
My OS is 10.7.5, My Arduino IDE ver is 1.0.5. When I created the project I told it to use source control and my board was the Mega 2560.