I'm not a Flash programmer, but this is my theory:
Whenever you minimize a Flash window, it "pauses" the window, as it is minimized and suggested not to be used, this is (I would think), to save CPU usage. This means the client isn't recieving packets (or as many), and cannot use aimbot because the packets aren't being recieved.
I was probably completely wrong, but that's a possibility. :3