If you minimize your Overseer window, close it, then re-open it, it can freeze your game window for a very long time as it takes forever to re-open the minimized window. Up to half an hour. Same thing happens if you zone when your Overseer window is minimized -- it can take up to 30 minutes to regain control of your character. I have around 2500 agents if that makes a difference. This problem started when they added the delay to Overseer transactions that makes your game freeze up for several seconds every time you add or remove agents. Except in this case we're not changing agents so I don't know why it's freezing your game session, or why minimizing the window causes a massive difference in behavior. The reason we sometimes need to minimize our Overseer window is because it's huge and covers a lot of the UI. If you forget that your Overseer window is sitting up there minimized, you get screwed by the game freezing behavior.
Not doubting the freeze, but I haven't noticed this behavior at around 1000 agents per account. I just tried most of mine and there were not any noticeable delays. Just trying to give them a lower bound... One thing that I found helpful after getting annoyed minimizing the window a lot. I set a key command for Overseers in the Options -> Keys area (it's under UI) and that way I can easily pull up the window (or make it go away) without having to minimize then trying to remember if I minimized or not.
