This issue sometimes happens if you have a short in a motor or motor controller - the rush of current to the motor causes a cortex reset. Try unplugging all the motors (and sensors) and see if you still have the issue.
If it goes away, plug in the motors one by one until the issue shows up again. Then you know where the issue is.
Also, check to make sure all the batteries in your joystick are facing the right direction and the same for the 9V battery.
Also, both the Cortex and Joystick don’t have the highest quality USB connectors - or at least they’re very easily abused. With the USB A-A cable, which has a narrow body, it’s easy to just slightly touch the key or cable and have it loose connection. This could be your case.
Also, Daniel, it’s a bit difficult to flip a 9V battery. Unless I’m forgetting something, everything is keyed.
If the solution isn’t fixed withe the taped vexnet keys, you might want to check your battery connection. With alot of the older VEX Cortex Microcontrollers the battery is easier to plug in and pull out than it is with a newer one. You can test this by gently shaking the connection of the battery into the cortex, if the lights come on and off, or the LCD screen blinks, or pnumatics trigger, then you are losing the connection between your battery and the cortex. So if you are driving and hit a small bump, or have vibration it will “reboot” as you put it. The only solution I have found for this is getting a new cortex, sometimes if one is faulty like this VEX will replace it.
We will try unplugging all the motors tomorrow and see what happens. We have found that if we slowly move the robot at first and then ramp up to full power it stays connected longer. If we move only one side of our tank drive it stays connected longer. If we move both joysticks to full power immediately, it reboots the cortex. We do not have loose batteries and the vex net keys seem solid. We have 4 robots and it is happening to all of them. I should say that our drivetrain is that each wheel has a single motor connected directly to each of 4 wheels. None of our robots have external gearing between the motors and wheels.