I think there may be a couple reasons why he is not green like everyone else.
1. If you are not created for this version of the matrix your code would not be the same as everyone elses. This would explain why agents are green. They come from this version they are their to protect that version. If we would have had a chance we would have seen all rogue programs not from this version would be yellow. Also the oracle and Arch. as well.
2. His program was written by someone other than the arch. and was added. The program language might be diffrent yet it was compatiable enough to use for this version of the matrix.
We have to keep in mind the matrix is a computer program like computers it has rules. It can be hacked and programed by anyone with the right tools. He might be gold because a human wrote him who knows.