Here's an excerpt from a Pattaya Today report:

"....It has also transpired that, in the calculation of the 90 days limit, all short term extensions are being included. If a foreigner, for example, chose to extend his 60 day prior tourist visa for a further month at a Thai immigration office, as he may, that one month extension would count towards the 90 days total allowance. Extra days given because of certified sickness should also be included in the counting up process...."

Full report:

Pattaya Today News

I have not seen any such report here on forum and believe we would have if it were the normal case (as almost everyone would be effected). I have seen that extensions of 30 day entry stamps were counted and believe overstay is also counted. But Pattaya is not a point of entry for many travelers so they may have there own drummer.