What should I do if my 90-day reports in Thailand have been repeatedly rejected despite receiving confirmation emails?

If you didn't notice your previous 90 day reports were rejected, you need to GO to the immigration office pay the 2000baht failure to file on time fine and file a 90 day report.

Especially if this happened THREE times when you tried to file a 90 day report and you never noticed it

Sounds like you just got the receipt of input. You need to check the receipt of approval which you can also do in the website but you need to select separately

It's a system issue at their end, the new website does not fill out the form properly. If you open the pdf it makes you can see the type of visa is not selected and a bunch of other bits, and not filling in the form fully is grounds for rejection. Then it's down to the officer that is processing the forms to determine the outcome

Superfluity info alert.

Using online reporting (after registering your account successfully), you may receive typically 4 types of emails. (of course, there are some more)

Mail subjects say:

1: [TM.47] (PASSPORT NO : XX56) FORM FOR ALIEN TO NOTIFY OF STAYING LONGER THAN 90 DAYS RECEIVED

<- means your 90 days report had been successfully submitted, but not get result yet.

you'd receive this email immediately after you submit your report.

2: [TM.47] (PASSPORT NO : XX56) FORM FOR ALIEN TO NOTIFY OF STAYING LONGER THAN 90 DAYS HAS BEEN REJECTED

<- means your 90 days report had been submitted but not approved.

3: [TM.47] (PASSPORT NO : XX56) FORM FOR ALIEN TO NOTIFY OF STAYING LONGER THAN 90 DAYS HAS BEEN APPROVED

<- means your 90 days report had been submitted but not approved. You also get 90 days report receipt as an attachment with the next 90 days reporting date.

4: [TM47] Notification for alien before the next appointment.

<- just a notification of your next due date sent 16 days before your due date. Your online reporting window starts the next day you receive this. This notification is not updated based on your travel abroad, just counting 90 days from the last reporting date.

You said you did three. So calculating days, your application for the next 1-year extension is coming up. When you go to apply for your extension, the office would tell you about your 90 days report. Follow their direction. Most likely you would do 90 days report on that time paying for a failed-to-report fine of 2,000 thb.