I have the same problem with a piece of c++ code. Running ubuntu 12.10 64bit. It looks to like a similar problem in 2007, where the libc was buggy (and maybe still is?).
I start a pthread which runs a traceroute in a system call. Printf before and after the system indicate, that the operating system hangs on the system call, WITHOUT executing the traceroute.
I am not sure if my linux is broken once again because of the ubuntu update, or if it's a libc related bug. Since a lot of applications seem to have "similar" problems, I assume it's stuck somewhere in the userspace.
My c++ code runs perfectly on 32bit systems and even 64bit osx, so i assume that ubuntu 12.10 + 64bit libc combination is broken.