I had no problems changing from an agent to getting my stamp at my local office once I had managed to meet all the criteria. The only thing my local office would not do is transfer my stamp to my new passport. They did not check that I had met the financial requirements for the previous year. I used a different bank account with the banked money which showed it had been there for three months prior to application. That was good enough. I'm not saying that this would be the case at every office.
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.