@Tod ********
I just had a similar experience with my 90 day report.
I had applied for my extension based on marriage.
On the date they had given me at the end of the pending period I went back in to immigration but was told that they were still waiting for authorisation from Bangkok and would call me.
A week went by and I was due to do a 90 day report. By this time my permission to stay had expired in my passport.
The Immigration officer couldn't do my 90 day report because on the system I was on overstay.
It was resolved by my new extension being stamped in and 90 day report issued.
I always do my 90 day reporting in person.