Exactly the same thing happened to me last week. Picked up my new 1 year visa and did my 90 days report after that with the new date. My 90 days report was a few days after due date but not over the 7 days allowed. No problem but very long queue.
Follow-up: back from visa renewal at Chaeng Wattana and no mention of either TM 30 or 90 days advice. They do, however, still insist on criminal record check for African passport holders.