wait .... If Opus/PC still running it has nothing to do with the remote entry. You may have to double check the connection. Unless Toyota is smart enought to disable the remote entry when there is a current drawn from the battery, but I don't think so because my Matrix remote entry lock the car okay while the PC is running.
Now for the 10 second thing. The 10 second is there because of the way the ACC wire in your car is wired. The power to this wire is cut off while you crank the engine. Normally the car only take couple seconds to start. If you change that time to 0 second or 1 second, the Opus will go to shutdown/hibernate when you crank the engine (ACC off = key out).
May be other peps explain it better