You haven't said which O/S you are running on and that might well have an impact here.

elseif ($signal_num != 0)

That isn't Perl, so either the code you are showing isn't the code you are running or your code isn't running at all.

The upper 8 bits had an exit code of 139, which indicates a seg fault, but the signal for seg fault was not set.

An exit code of 139 does not necessarily indicate a seg fault. Trivially:

#!/usr/bin/env perl 
use strict;
use warnings;

system ('perl -e "exit 139"');

my $exit_value  = $? >> 8;
my $signal_num  = $? & 127;
my $dumped_core = $? & 128;

print <<EOT
Exit value: $exit_value
Signal:     $signal_num
Core:       $dumped_core
EOT
[download]

Is there a module or library I can use to automatically catch all of the "bad" return values so I don't have to code all of the enumerations of signals and return values myself?

Unlikely because your idea of "bad" may not be someone else's idea of "bad". However, you could simply write your own module for your own use and then use that in all your other code.