Uhh, am I missing something?

use strict;
use warnings;

print scalar localtime, "\n";

eval {
    $SIG{__DIE__} = sub { alarm(0) };
    $SIG{ALRM} = sub { die "timeout" };
    alarm(2);
    system('sleep 5');
};

print $@ if $@;
print scalar localtime, "\n";
[download]

Output:

Fri May 22 17:46:53 2015
timeout at C:\Temp\b.plx line 8.
Fri May 22 17:46:55 2015

Alarm appears to work just fine even when calling out to system