How to get compatibility between C# and SQL2k8 AES Encryption?

I have an AES encryption being made on two columns: one of these columns is stored at a SQL Server 2000 database; the other is stored at a SQL Server 2008 database.

As the first column's database (2000) doesn't have native functionality for encryption / decryption, we've decided to do the cryptography logic at application level, with .NET classes, for both.

But as the second column's database (2008) allow this kind of functionality, we'd like to make the data migration using the database functions to be faster, since the data migration in SQL 2k is much smaller than this second and it will last more than 50 hours because of being made at application level.

My problem started at this point: using the same key, I didn't achieve the same result when encrypting a value, neither the same result size.

Below we have the full logic in both sides.. Of course I'm not showing the key, but everything else is the same:

private byte[] RijndaelEncrypt(byte[] clearData, byte[] Key)
{
    var memoryStream = new MemoryStream();

    Rijndael algorithm = Rijndael.Create();

    algorithm.Key = Key;
    algorithm.IV = InitializationVector;

    var criptoStream = new CryptoStream(memoryStream, algorithm.CreateEncryptor(), CryptoStreamMode.Write);
    criptoStream.Write(clearData, 0, clearData.Length);
    criptoStream.Close();

    byte[] encryptedData = memoryStream.ToArray();
    return encryptedData;
}

private byte[] RijndaelDecrypt(byte[] cipherData, byte[] Key)
{
    var memoryStream = new MemoryStream();

    Rijndael algorithm = Rijndael.Create();

    algorithm.Key = Key;
    algorithm.IV = InitializationVector;

    var criptoStream = new CryptoStream(memoryStream, algorithm.CreateDecryptor(), CryptoStreamMode.Write);

    criptoStream.Write(cipherData, 0, cipherData.Length);

    criptoStream.Close();

    byte[] decryptedData = memoryStream.ToArray();

    return decryptedD