I just had the 8100NEX installed on my 2012 vw cc at a car audio shop this morning. The shop was at a loud and noisy crossroad so I didn't notice this noise while I was checking the car. 

The noise is much like a buzz or a white noise coming from the position of the a/c. But I am sure that the problem is not the a/c. It happens when car is ignited or in ACC mode and it goes away when I completely shut the engine off. I also see a "System detected improper connection of parking brake lead. Please check your configuration for safety. Please see operation manual for more information regarding safe operation." message.

Since the noise was really annoying and the more I tried not to pay attention to, the more annoying it gets. I updated the firmware from 1.01 to 1.03 the second I got home. But the problem still exists. 

Anyone encountering the same problem? Anything would be helpful.

Take it back to the shop

You have what is known as alternator whine. You need a to buy a ground loop isolator or run your power wires opposite the side you run you speaker cables. This happened to me when I bought the avic d3 and had two amps one for the subs and one for the speakers.  I bought this a few years back from Walmart which solved the issue. http://www.walmart.com/ip/Scosche-ES034-GROUND-LOOP-ISOLATOR/896355

When you take it back to the shop, tell them that the bypass on the 8100nex is software only and they should hook the brake wire up correctly. See the bypass sticky thread on how to enable bypass.

You need a to buy a ground loop isolator

Don't do this. It is a cheap audio transformer, and it will ruin your bass, highs, and transient response.

If the sound is indeed coming out of your speakers (which it doesn't sound like based on your description), you have a grounding problem which needs to be addressed by the installer, and not via a cheap and dirty transformer.

Take the installer out for a test drive so he can hear it.

When you take it back to the shop, tell them that the bypass on the 8100nex is software only and they should hook the brake wire up correctly. See the bypass sticky thread on how to enable bypass.

Yup.

there is a know issue with first generation software causing noise. Try installing the new firmware update. you can download free off the Pioneer site.