Thanks PodMaster, that was it precisely. I rewrote the programs as follows:

encode_base64.pl:

#! /usr/bin/perl
use strict;
use MIME::Base64 qw( encode_base64 );

open INFILE, '<', $ARGV[0];
binmode INFILE;
open OUTFILE, '>', $ARGV[1];
my $buf;
while ( read( INFILE, $buf, 60 * 57 ) ) {
    print OUTFILE encode_base64( $buf );
}

close OUTFILE;
close INFILE;

__END__
[download]

decode_base64.pl:

#! /usr/bin/perl
use strict;
use MIME::Base64 qw( decode_base64 );

open INFILE, '<', $ARGV[0];
open OUTFILE, '>', $ARGV[1];
binmode OUTFILE;
my $buf;
while ( $buf = <INFILE> ) {
    print OUTFILE decode_base64( $buf );
}

close OUTFILE;
close INFILE;

__END__
[download]

The PDF decoded correctly this time. Thanks!