It's not obvious that the subprocess module is doing anything wrong here. Mixing streams and file descriptors is always problematic and should best be avoided (http://ftp.gnu.org/gnu/Manuals/glibc-2.2.3/html_node/libc_232.html). However, the subprocess module *does* accept a file object (based on a libc stream), for convenience. For things to work correctly, the application and the subprocess module needs to cooperate. I admit that the documentation needs improvement on this topic, though. 

It's quite easy to demonstrate the problem, you don't need to use seek at all. Here's a simple test case:

import subprocess
rawfile = file('hello.txt', 'rb')
rawfile.readline()
p = subprocess.Popen(["cat"], stdin=rawfile, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
print "File contents from Popen() call to cat:"
print p.stdout.read()
p.wait()

The descriptor offset is at the end, since the stream buffers. http://ftp.gnu.org/gnu/Manuals/glibc-2.2.3/html_node/libc_233.html describes the need for "cleaning up" a stream, when you switch from stream functions to descriptor functions. This is described at http://ftp.gnu.org/gnu/Manuals/glibc-2.2.3/html_node/libc_235.html#SEC244. The documentation recommends the fclean() function, but it's only available on GNU systems and not in Python. As I understand it, fflush() works good for cleaning an output stream. 

For input streams, however, things are difficult. fflush() might work sometimes, but to be sure, you must set the file pointer as well. And, this does not work for files that are not random access, since there's no way of move the buffered data back to the operating system. 

So, since subprocess cannot reliable deal with this situation, I believe it shouldn't try. I think it makes more sense that the application prepares the file object for low-level operations. There are many other Python modules that uses the .fileno() method, for example the select() module, and as far as I understand, this module doesn't try to clean streams or anything like that. 

To summarize: I'm leaning towards a documentation solution.