update: meh, I see you've already tried what I have below...

update2: I can't reproduce what you're seeing (test exits):

use Test::Exception tests => 2;
use Test::More;

sub blah {
    die "died!";
}

throws_ok { blah() } qr/died!/, 'died ok';
is (1, 1, 'one is one');

__END__
ok 1 - died ok
ok 2 - one is one
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/updates

Isn't:

$logger->fatal("(Line: $line) " .  $error);
die "\n";
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Simply logging a message, and then die()ing with only a newline character being set to $@, which I presume that throws_ok() will see?

Does:

$logger->fatal("(Line: $line) " .  $error);
die "(Line: $line) " . $error;
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help?