Losing bytes while decrypting with Rijndael

Question

I wondered if somebody would like to help me solve the following problem:
I'm trying to decrypt a file which is 32 bytes long before the decryption process. After the the decryption process, just 16 of the 32 bytes remain. All of the 16 bytes are decoded correctly! Does somebody know how i can prevent such a loss of data?
Here follows a code-snippet:
byte[] enckey = "thisisabeautifullkeydontyouthink".getBytes();
SecretKeySpec key = new SecretKeySpec(enckey, "Rijndael");
System.out.println("Loaded the key.");
// Create a cipher using that key to initialize it
Cipher cipher = Cipher.getInstance("Rijndael/CBC/PKCS5Padding");
FileInputStream fis = new FileInputStream("c:\\temp\\foo.dat");
FileOutputStream fos = new FileOutputStream("c:\\temp\\decrypted_foo.dat");
byte[] iv = "thisstringislong".getBytes();
IvParameterSpec spec = new IvParameterSpec(iv);
System.out.println("Initializing the cipher.");
cipher.init(Cipher.DECRYPT_MODE, key, spec);
CipherInputStream cis = new CipherInputStream(fis, cipher);
System.out.println("Decrypting the file...");
int theByte = 0;
while ((theByte = cis.read()) != -1)
fos.write(theByte);
cis.close();
fos.close();
I hope somebody is able to help me out!
Thanks in advance,
Mathieu

Answer 1

I didn't use padding encode my files, so i've changed my cipher.init to Cipher cipher = Cipher.getInstance("Rijndael/CBC/NoPadding"); Now the cipher does not produce any errors when decrypting. Still the output differs slightly from the original file.
For encoding my files i use perl. Is there a possibility to decode my files using the java.cipher? If so, what parameters should I use for decoding my files? Here follows my Perl code:
sub encrypt{
    my ($key, $file, $file_out) = @_;
    my $buffer;
    # Rijndael encryption module
    use Crypt::Rijndael;
    $cipher = new Crypt::Rijndael $key, Crypt::Rijndael::MODE_CBC;
    # Open files
    open INF, $file;
    open OUTF, ">$file_out";
    # Binairy mode
    binmode INF;
    binmode OUTF;
    # Set IV
    $iv="mijnnaamishaasje";
    $cipher->set_iv($iv);
    # Read in and write
    while (
      read (INF, $buffer, 1024) and
             print OUTF $cipher->encrypt(get16($buffer))
    # Close files
    close OUTF;
    close INF;
sub get16 {
    my $data = shift;
    if (length($data)%16==0) {
        $return = $data;
    else {
        $return = $data . "\0" x ( 16 - length($data) % 16 );
    return $return;