As an addendum to this topic, I just got back from Samut Prakan Immigration. It was very crowded and we waited 2 hours and that was with an appointment. The officer looked at my documents and noticed there was the agent in Chonburi and the lacking evidence that goes with using an agent. We then got lectured by the officers' boss for 15 minutes, I am not exaggerating, it was 15 minutes. So now I have to leave the country and get a new visa.
If anyone tries to switch from using an agent to trying to go legit, you may well have problems, especially in lovely Samut Prakan.