On Linux:

>>> p = subprocess.Popen("ls", stdout=subprocess.PIPE)
>>> p.stdout.read()
b'...'
>>> p.stdout.seek(0)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/heimes/dev/python/py3k/Lib/io.py", line 809, in seek
    pos = self.raw.seek(pos, whence)
IOError: [Errno 29] Illegal seek
>>> p.stdout.read()
b''

On Windows p.stdout.seek(0) does neither raise an error nor works as one
might expect it. The second read() returns an empty byte string, too.

Python 2.5 on Windows has the same behaviour, it does not fail.
In general, python does not try to hide this kind of differences.

@Brian/Tim what would you expect to happen here?

Looks like it's a platform bug, nothing Python can do about.