I've never seen that message before. I did my first 90 day report on line without an issue on returning from UK. 90 day reports are usually rejected because tm30 is not up to date so does not tally with the address put on the application.
Strangely my immigration office do not issue a certificate of redidence for this. I have to go to land transport and they request a certificate of residence which takes about a week. Same thing when changing blue book for the car I bought.