Hey,
Can someone please help? Every time I pair the cortex to the joystick via VEXnet it connects fine but as soon as I download the program time cortex does not link to the joystick via VEXnet. I've re-paired several times and every the same thing happens. Everything is updated so what now?

Have you gone through our 'Getting Started with the VEX Cortex (VEXNet)' guide on the ROBOTC wiki? It can walk you through, step by step, how to set up the VEXNet connection between a Cortex and a VEXNet controller. Of particular importance is Step 4, 'Setting Cortex Communication Mode'; this step is often overlooked and could be the cause of the issues you are seeing.

Let us know if this solves the issue for you, and if not we will continue to assist you in getting it working properly.