Wasn't waiting for POpen to complete: POpen forks a separate process, so to read in all the output reliably, you need to wait for the process to complete.
Couldn't locate coffeedoc on PATH on Windows: POpen doesn't spawn a shell process by default, so even when coffeedoc is on the PATH, it couldn't find it (at least on Windows). I would have expected this to be the case on unix as well, but haven't got a machine to hand to test that with at the moment.
Thanks for the patches, the different output format has already been fixed but I hadn't yet pushed up my changes. There's actually a number of improvements coming up including showing inheritance for classes and inheritance across modules as well.
Regarding Popen.wait, I think this might also be windows-specific. I wasn't using wait() before because of this warning in the python docs: http://docs.python.org/library/subprocess#subprocess.Popen.wait, but if popen.stdout.read() doesn't reliably retrieve all output on windows I'll use popen.communicate instead.