When I did my last 1 year extension, the IO also did a 90 day report even though it wasn't really due. About 30 days later, I got an email reminder informing me that my online 90 day report was due, which was based on my previous online reporting date. I simply ignored that email and did my next online report (which was accepted and approved) to correspond with the date on the receipt that I got for the manual report done by the IO. No problems arose. It's not me that's advising you when to do the report. The rule is that you need to do a 90 day report only if you have been in the country for 90 consecutive days. Your next report should contain your latest date of entry into Thailand. Also there is no way I can predict if your IO will be confused or not.