I had something like this too but it doesn't work on Windows. Here is a stripped down example using Inline::C. On non-Windows (cygwin included), it outputs correctly:
On Windows, it gives:
which shows you that the STDERR isn't being captured.
use File::Temp qw(tempfile);
use Inline C;
open my $olderr, '>&STDERR'; # save STDERR
my ($fh, $fn) = tempfile();
open STDERR, '>&', $fh;
open STDERR, '>&', $olderr; # reset STDERR
open my $e, '<', $fn;
my $err = <$e>;
(void)fprintf (stderr, "ERROR");
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