Here is "proof" perl (or perlxs) is stuffing stderr into a buffer

#!/usr/bin/perl --
use Inline C => Config =>
    BUILD_NOISY => 1,
#~     FORCE_BUILD => 1, 
    CLEAN_AFTER_BUILD => 0,
; # Inline

use Inline C => <<'__C__'; 
void test_err()
{
    PerlIO_printf( PerlIO_stderr(), "Inline::C PerlIO_printf => PerlIO
+_stderr()(%p) is PerlIO_fileno()(%d)\n", PerlIO_stderr(), PerlIO_file
+no(PerlIO_stderr()) );
    fprintf (stderr, "Inline::C fprintf => PerlIO_stderr()(%p) is Perl
+IO_fileno()(%d)\n", PerlIO_stderr(), PerlIO_fileno(PerlIO_stderr()) )
+;
    fprintf (stderr, "Inline::C fprintf => stderr(%p) is fileno(%d)\n"
+, stderr, fileno(stderr) );
// above output gets eaten if you flush
//    fflush (stderr );
    fprintf (stderr, "will somebody please eat my stderr buffer \n");
}
__C__

Main( @ARGV );
print "main is over\n";
exit( 0 );
END { print "perl is over\n"; }

sub Main {
    use FileHandle;
    STDERR->autoflush(1);
    STDOUT->autoflush(1);
    use File::Temp qw' tempfile ';
    open my $olderr, '>&STDERR'; # save STDERR
    my ($fh, $fn) = tempfile();
    open STDERR, '>&', $fh;

    test_err();

    open STDERR, '>&', $olderr; # reset STDERR
    close $fh;

    open my $e, '<', $fn;
    my $err = <$e>;
    print "(((($err))))\n";
}

__END__

[download]

without fflush

((((Inline::C PerlIO_printf => PerlIO_stderr()(99417c) is PerlIO_filen
+o()(2)
))))
main is over
perl is over
Inline::C fprintf => PerlIO_stderr()(0099417C) is PerlIO_fileno()(2)
Inline::C fprintf => stderr(77C5FCC0) is fileno(2)
will somebody please eat my stderr buffer
[download]

with fflush

((((Inline::C PerlIO_printf => PerlIO_stderr()(99417c) is PerlIO_filen
+o()(2)
))))
main is over
perl is over
will somebody please eat my stderr buffer
[download]

And doing the same thing WITHOUT perl , code from _dup, _dup2 adapted for mingw-gcc

// crt_dup.c
// This program uses the variable old to save
// the original stdout. It then opens a new file named
// DataFile and forces stdout to refer to it. Finally, it
// restores stdout to its original state.
//

#include <io.h>
#include <stdlib.h>
#include <stdio.h>

int main( void )
{
   int old;
   FILE *DataFile;

   old = _dup( 1 );   // "old" now refers to "stdout" 
                      // Note:  file descriptor 1 == "stdout" 
   if( old == -1 )
   {
      perror( "_dup( 1 ) failure" );
      exit( 1 );
   }
   _write( old, "This goes to stdout first\n", 26 );
   if( fopen_s( &DataFile, "data", "w" ) != 0 )
   {
      puts( "Can't open file 'data'\n" );
      exit( 1 );
   }

   // stdout now refers to file "data" 
   if( -1 == _dup2( _fileno( DataFile ), 1 ) )
   {
      perror( "Can't _dup2 stdout" );
      exit( 1 );
   }
   puts( "This goes to file 'data'\n" );
   system( "echo echo echo echo echo echo echo" );
   system( "echo echo this goes to 'data' " );
   system( "perl -le print(666)" ); // goes to data

   // Flush stdout stream buffer so it goes to correct file 
   fflush( stdout );
   fclose( DataFile );

   // Restore original stdout 
   _dup2( old, 1 );
   puts( "This goes to stdout also\n" );
   puts( "The file 'data' contains:" );
   _flushall();
   system( "type data" );
}

//~ EUREKA http://v8.googlecode.com/svn/trunk/src/platform-win32.cc
int fopen_s(FILE** pFile, const char* filename, const char* mode) {
  *pFile = fopen(filename, mode);
  return *pFile != NULL ? 0 : 1;
}
[download]

as you can see it works

This goes to stdout first
This goes to stdout also

The file 'data' contains:
echo echo echo echo echo echo
echo this goes to 'data'
666
This goes to file 'data'
[download]

If I knew more about gcc and debuggers, I might try to figure out WHERE perl fudges things , but I don't :)