@Max *******
The system is a tad fickle. However, it sounds like more issues happen with those on exemptions versus those on an actual visa. The issues individuals have with their exemptions are when the IO suspects you are living in Thailand. Some flags for them can be 1-day border hopping, length of stay adding up, etc. unfortunately, it sounds like this OPer ended up being called out for a visa run and now it is marked in the system