I didn't mean to imply anything about subprocess.check_output().  It works as expected, that is by explicitly intercepting anything written to the stdout of the forked subprocess and returning it as the call result.  What doesn't work is if you try a default subprocess.call(), for example.  The results are the same as os.system and for the same reason.  In a Posix terminal session:

$ python3.3
>>> import subprocess
>>> subprocess.call('pwd')
/Users/nad
0
>>> 

But in an IDLE shell window:
>>> import subprocess
>>> subprocess.call('pwd')
0
>>> 

That's confusing to users.  IDLE should handle that.