I don't see $cipher->finish anywhere. Read the Crypt::CBC man page. $cipher->finish must be called after the last $cipher->crypt() to flush the buffer out. That's why the last line isn't making it to the file.

Update:I think I need to elaborate.

if ($mode == 0) {
    open(INFILE, "<$inFile") || die "Error opening source file for inp
+ut! \n";
    open(CRYPTFILE, ">$cryptFile") || die "Error opening crypt file fo
+r output! \n";
    $cipher->start('encrypting');
    
    while (<INFILE>) {
        print CRYPTFILE $cipher->crypt($_);
    }

        print CRYPTFILE $cipher->finish;

close INFILE;
close CRYPTFILE;
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BMaximus