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This seems to be a Cygwin bug: p.stdout.read() only returns
a partial result. Another p.stdout.read() is necessary to
retrieve all data. fileobject.read should return all data,
though. It doesn't, because fread() is behaving strange: It
returns a short read, but neither feof() nor ferror() is
set. This is wrong:

"Upon  successful  completion, fread() shall return the
number of elements successfully read which is less than
nitems only if a read error or end-of-file is encountered."

One strange thing is that this only happens if close-on-exec
is used for the error pipe. Perhaps a race condition.