This is an unfortunate situation. If Immigration had raised the overstay issue in March, it could have been dealt with with only a fine. A handful of well connected agents are allegedly able to finesse the problem, but I understand the costs are now astronomical. I assume you do the 90-day address reports yourself, not using Thailand Elite. If so, there is no way Thailand Elite could be expected to know about your issue. As others have posted, the requirement to request an extension if in Thailand over one year is well documented.