I'm having a vaguely similar problem. Perhaps what I found might help you out. What i was seeing was that this code snippet would fail with "Bad file descriptor" on XP (works fine on W2K):

delete $ENV{PATH}; # for taint mode
open ( CMD, '/tools/usr/local/wbin/ls.exe / 2>res.txt |' ) || die $!; 
while ( <CMD> ) { print; }
close ( CMD );
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Any of these changes allow the program to run:

1. remove the redirect of STDERR
2. remove the delete of the PATH envar
3. set the PATH (rather than delete it) to

$ENV{'PATH'} = 'C:/WINDOWS/system32;';
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Yes, this last one is not good and I'm not sure what executable is being run from there or DLL being loaded. (strace for Windows?) Anyway, I know this isn't exactly your problem but maybe it will give you some ideas.

- Mike