The problem is that you are not having IPC::Run manage any I/O. If you set the timeout to a large value (like 20000), run your program and do an strace on the perl process you'll see that IPC::Run is stuck in the following select call:

$ strace -p1625
Process 1625 attached - interrupt to quit
select(0, NULL, NULL, NULL, {19943, 944000}
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Just change your code so that some pipe between parent and child is closed when your child exits. Then IPC::Run will notice your child's exit. Example:

use IPC::Run qw(run timeout timer);

my $t = timeout(20000);
my $out;
run(debug => 1, ["/bin/sleep", 5], '>', \$out, $t);
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Update: Another solution is to simply install a CHLD signal handler. It doesn't have to do anything -- the mere fact that the signal is not ignored will cause the select call to be interrupted:

$SIG{CHLD} = sub {};
run(["/bin/sleep", 5], timeout(20000));
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