IPC-Run3 is in activestate repository. Maybe this does what you need?
http://matrix.cpantesters.org/?dist=IPC-Run3+0.042

#!/usr/bin/perl -w
use strict;
# running Active state 5.10

use IPC::Run3;

run3 ("dir C:/");
[download]

works fine.
Sounds like you just need Run3 instead of just simply "run".

Update:
if you read the params to run3, you can give it handles for stdin, stdout, stderr, etc. run3 appears to be implemented on *nix as well as Windows, so I don't think you need any special Windows vs *nix code.