I install the controller firmware on the joystick, and install the master firmware then the normal firmware to the cortex. After this I tether the two together and get(on the joystick) a red joystick light, and green robot and vexnet lights. On the cortex I get 3 green lights. everything should be tethered. I then plug the keys back and and turn on both of them and I get a slowly blinking green light on the joystick and flashing yellow ligts for vexnet and game on the cortex. Occaisionally the joystick will flash all red for a second or all the lights will turn red and stay red. It seems like its untethering or something. I cant download after this or control anything. Also I can only download the firmware from one of my computers. The other computer doesnt seem to recognize the cortex even thought it used to. Any suggestions? thanks!
I have heard (haven’t looked into this to make sure) that all red on the joystick means dead joystick battery, so you should try replacing them. This would make sense as you said it gave a red joystick light.
~Jordan
I agree with Jordan – the first thing I would try is replacing the joystick batteries.
xD yep it was dead batteries, thanks a bunch
Glad to hear that worked! And no problem, anytime. 
~Jordan