That makes no sense. run doesn't care at all about line endings.

use strict;
use warnings;

use IPC::Run qw( run );

my @cmd = (
    perl => (
        -e => 'print "x" x 100_000',
    )
);

run \@cmd, \'', \my $out, \my $err
    or die("Error returned by $cmd[0]: $?\n");

print("Receveived ", length($out), " chars\n");
[download]

$ perl a.pl
Receveived 100000 chars
[download]

What don't you start by doing some error checking? What does run return? What does $? contain after run? Are you getting an exception from run or from the timeout?