I have used the online system with no problem for some time. In early August I returned from a trip to UK (re-entry permit). 90 days was due last week so 8 or 9 days before, I submitted an online report, which was accepted and shown as "pending". As it went a week without confirmation I cancelled it and re-submitted, again shown as "pending". On the due day it was still outstanding so I printed off the acknowledgement and went along to Immigration. I was quickly handed a receipt with the next reporting date and out of the building in less than a minute.
As it was dealt with so quickly and I'm only a short drive from the office I didn't bother to query why they hadn't dealt with my online submission. However, I have since recalled that in September we had a trip to Isaan, and one of the hotels we stayed in would not accept my driving licence and insisted on copying the copy of my passport on my phone (as I wasn't carrying my passport). Presumably they submitted this to local Immigration, so that the Rayong office looked at the computer and decided that after returning from Blighty I might have gone to live in Khorat - although the online report clearly showed my address as it has been for the last 13 years.
I suppose it's too much to expect hotel check-in staff to distinguish between tourists and longer-staying residents.