Them having told you that you had to file a new form is inconsistent with everything I have read on the subject. That they did not accept the form tends to support the idea that the 90 day count starts over on the day you re-enter the country.
The TM card that we hand in when we enter the country serves as your initial notification of your address, then we just need to let them know every 90 days after that.
It might be that they wanted you to come in so they can see your face, say "hello" and remind you who it is that you have to be grateful to for your stay in Thailand. Or, it could have been miscommunication. (Or category C: none of the above

)