I'm sorry to hear of your dilemma, and as a former CA resident, I empathize with your predicament.
Under CA law, even pushing a non-op vehicle on a roadway is considered operating it. I will presume that your son somehow moved the vehicle off of private property and onto public property. How the DMV found out about it is the big mystery. If I had to guess, I would guess that the vehicle was perhaps left on the street for a period of time, perhaps received a citation of some sort like out of date registration?
The reality is that if you can prove that the vehicle never touched public property, nor was it transported over public property---as would be the case if it were towed anywhere---then the fine is valid.
Get the vehicle back on private property, pay the fine and re-file the non-op status. That is really about all you can do---I'm sorry.
I wish you the best in 2010.
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