I had similar 90 day reporting issues after travelling overseas during May. This was my 1st trip for about 6 years and had been reporting online with no hassle previously. That changed with the overseas trip and, having read through the recent posts I had resigned myself to making a trip to Jomtien.
Last week was the deadline to report and I decided, at the last minute, to make use of the services of a well known agent on Soi 13/2. So, paid Bt100 and collected my passport / 90 day report a day or 2 later. For me, definitely the best option and, hopefully, I am now back on track to make use of the online reporting portal.