I seem to recall, from a project in the not too distant past, that we had a similar mountain to climb using Strawberry Perl 5.8.8.
IIRC, since perl (c/w the shell) handles any redirection, the problem was easily resolved using open() in conjunction with standard *NIX redirection (ignoring '-' as a stdin/stdout designator) e.g.

open CMD, "command 2>&1 |" or die "Couldn't open() command - $!";
while (<CMD>) {
  .
  .
[download]

HTH,