That's incorrect. 90 days starts from the day a visa or extension inside the country is issued. IF you leave the country and reenter, your 90 days will restart from the date you entered. Since Chris was issued a new extension of stay after he entered the country, his next 90 day report is from the date the extension was issued.
If your yearly extension was issued on June 1st then your 90 day report is due 90 days from then. Unfortunately you're going to have to make a trip down there and deal with it, should just be a paper work thing, can't see them fining you. I'd wait until Wednesday though, Monday it will be a mad house.
Unfortunately no, and you're not alone. Unless you fall into the specific class of people currently permitted to enter Thailand, then it's still closed.