ISO 9797-1 MAC Algorithm 3 consists of using the first DES key to perform a CBC MAC and then only for the final block perform a full 3-DES operation.

Try this:

byte[] keybytes = ParseHex(key);
byte[] key1 = new byte[8];
Array.Copy(keybytes, 0, key1, 0, 8);
byte[] key2 = new byte[8];
Array.Copy(keybytes, 8, key2, 0, 8);

DES des1 = DES.Create();
des1.Key = key1;
des1.Mode = CipherMode.CBC;
des1.Padding = PaddingMode.None;
des1.IV = new byte[8];

DES des2 = DES.Create();
des2.Key = key2;
des2.Mode = CipherMode.CBC;
des2.Padding = PaddingMode.None;
des2.IV = new byte[8];

// MAC Algorithm 3
byte[] intermediate = des1.CreateEncryptor().TransformFinalBlock(data, 0, data.Length);

// Output Transformation 3
byte[] intermediate2 = des2.CreateDecryptor().TransformFinalBlock(intermediate, intermediate.Length - 8, 8);
byte[] result = des1.CreateEncryptor().TransformFinalBlock(intermediate2, 0, 8);