Hum, I just ran into this issue this morning with downloaded code and that fixed it for me. I'm at a bit of a loss as to why it's not working for you. Try deleting your game completely and rebuilding it after running this command if you haven't already.
@matt, I did try all the above without any luck so far. It is interesting that doing a 'build' command, followed by a 'run' command from Xcode it will succeed.
Need to get some time to look at what happens in the run step in Xcode to see if I can isolate what is changing. Part of me wonders if it is a timing thing, like perhaps if the launch to the sim was a little delayed would it work in one step?
The zero-byte pdex.bin also happens when make is doing parallel builds, because there's a bug in our C_API/buildsupport/common.mk file: The pdc target should depend on device as well as simulator so that it finishes compiling pdex.bin before running pdc.