I just did a quick search on google and found this other site where others where also having problems with their VIN number not showing valid on Toyotas' website. Might want to maybe call the dealership service deptarment and see if they can square you away on it. Here is the link where I read they too were having problems with their VIN number:
I remember getting a notice in the mail for my old '94 for this. I never did have it done, and never had any problems, either--I kinda' looked at it this way, if the darn thing already made it over 200k miles, it's proven itself to be every bit as strong as the rest of the hardware. But, I guess if it's free, what the hey...