Your 90 report is based on your arrival date in Thailand or your previous 90 say report. Visits to immigration that do not involve 90 day reporting do not count as a 90 day report. In the eyes of immigration the 90 day report is a stand alone document
The Manila Embassy says issued 72 hours prior to the scheduled departure time of your first registered flight on your COE. in my case I had 3 flights on 3 concecutive days