I made some progress tonight. I swapped the 16 pin connector with the 20 pin and connected to the OBD port inside the engine room. Guess what? it worked!!! the programming was very straightforward.
Thanks Jose for your inputs.

I think that later models may not have an OBD port under the hood or the pin layout might be different than the older one like mine. Anyway, it worked for me. Great!

However, the problem with my 330ci persists. I am pretty sure it does not have a second OBD port inside the engine room (need to do some research), so it may not be easy to troubleshoot it without expert's inputs from you guys.