SF Non-moving violation, double jeopardy for "fix it" ticket already being fixed?

I received a non-moving parking violation for missing registration stickers in December (the tabs either fell off or were stolen, my car was registered). While protesting the ticket and ordering a replacement sticker from the DMV, I received 2nd ticket for the same thing in January. I sent in a protest for the 2nd ticket the same day I paid the $10 fine for the 1st ticket with proof from the DMV and a signed letter from a SF police officer that the problem had been fixed. The problem has two parts; (1) MTA says they never received the protest for the 2nd ticket and (2) they are saying I have to pay the full price ($142) for the 2nd ticket. Isn’t this double jeopardy? Anyone know what I can do?