I just got to a point where I don't get errors anymore. Here's what I did.

First, I modified the way I create the Crypt::CBC object to:
my $cipher = Crypt::CBC->new(-key => $self->{SYMMKEY}, -cipher => 'Twofish', -salt => 1) or die "Unable to create cipher:\n$@\n";

My undertsanding is that CBC is now using a random Salt instead of a random IV. Correct me if I am wrong.

Doing that solved the decryption error I was getting. It was replaced by an EOCD error during the unzip operation.

I then followed your suggestion and replaced the getline with read:

# $fh_cipher->write($cipher->crypt($fh_plain->getline)) until ($fh_pla
+in->eof);
do {
    $fh_plain->read($buf, length($self->{SYMMKEY}));
    $fh_cipher->write($cipher->crypt($buf))
} until ($fh_plain->eof);
[download]

and:

# $fh_plain->write($cipher->crypt($fh_cipher->getline)) until ($fh_cip
+her->eof);
do {
    $fh_cipher->read($buf, length($self->{SYMMKEY}));
    $fh_plain->write($cipher->crypt($buf))
} until ($fh_cipher->eof);
[download]

That got rid of the EOCD error. My app now runs as expected. Thanks for the tip!