As far a i know if you have ltr you do not have to file 90 days! I have one and never do that. Only one time every year but if you are not a year in Thailand you do not have to do that!
I agree came in two weeks ago and the ltr visa was mentioned ! But some of the , mostly girls, who check if you are allowed are sometimes not really well informed. Just ask for a higher up official
As said when you leave Thailand before 90 days the counting starts at 1 when you enter Thailand. And if you do not want to exceed the 180 days in Thailand just count the days.