theres a bug when using the load in robot button, if you press this button right after the code has been uploaded to the robot it starts executing the code, even if the hole execution is paused, this bug is pretty annoying when your code has to do some calibration at the start because you dont know when the code will start
As you state, the robot brain is always running despite the simulation being paused. We will work on stopping the brain execution for following versions.
If you want to ensure that the simulation is running when you start the brain, we suggest you to run an empty code:
from GUI import GUI
from HAL import HAL
#Enter sequential code!
#Enter iterative code!
In order to unlock the Start button (or before pressing Reset if it is not the first attempt), then start the simulation and load your desired code.