I suggest that you update your developer tools, then. Xcode 3.1.3 is not supported (by Apple) on Snow Leopard.

Interestingly, an existing C++ project in Xcode 3.1.3 on Snow Leopard (which also uses a Jamroot file) does compile and run fine.
Yes, I intended to upgrade but I am surprised that compiling with Xcode 3.1.3 does work but using the command line does not.