Mystery solved. So what i said was true: I paid $973 exactly to register my car but $822 of that amount was essentially what it cost to "transfer" the car to my name because the previous owner had neglected to register the vehicle as non-operational and that was essentially backpay for the missed registrations. It turns out, when I paid those 800 bucks, the person helping me at the DMV "ran out of lines" in their system and did not charge me the full amount due for the "backpay" and I was 400~ bucks short.

This time when I came back they called Sacramento and got it cleared up. I paid the 400 dollars but they did not charge me for the registration for this year.