OK, If I understand the issue, I would say that in your situation, the Microsoft person, that you talk to, was incorrect.
If a computer is bought with Vista pre-installed, and then the user changes out the motherboard, then you can not continue to use the same Vista license, but if the "computer builder" was the one to change out the motherboard, then you Can continue to use the same Vista license.
So, in your situation, it soulds like you bought the computer and the Vista software seperatly and installed Vista on the computer, yourself. In that case, you are now seen as the "Computer Builder" and since you (the computer builder) changed out the motherboard, you CAN continue to use the same Vista license.
I suggest that you follow the below steps to re-activate you copy of Vista:
1) Click the Start button
2) Type: slui.exe 4 and hit the 'Enter' key
3) Select the area that you are located in.
4) Follow the steps provided by Activation Wizard
NOTE: The key to this process is that you need to talk to a Live Activation Rep! When you first call, you will be interacting with an Automated Voice, either select the option to talk to a Live Rep or if there is no option, do not enter any numbers. This should force the automated voice to tansfer you to a Live Rep. I Highly suggest that you DO NOT mention that you changed out your motherboad, it will only confuse the Rep. Just say you need to Re-activate because you changed out some "hardware" in your computer.
WGA Forum Manager