I am experiencing a loss of communication between the Joystick and Cortex at random times. What can I do to prevent this?

Can you be a little more specific about what you men by communication loss? Does the connection actually drop out and reset, or does the robot just not respond to specific joystick input for a short time? I only ask to make sure that it's hardware based, and not something in the code that makes it seem like you're experiencing communication loss. If it's hardware based, make sure that your key isn't enclosed by metal on your robot. Try placing it up and out of the way so it has clear range. For the VEX competition, it is legal to use a small USB extension to mount your key somewhere other than directly in the Cortex slot. It is also possible that you have a bad key (they're not known for their reliability). Try swapping them out with different keys and see if the problem persists.

I think its hardware. The USB keys could be disconnecting through movement. I will try the extension. For competitions, can any type of extension be used or does it have to be VEX?

You can use any USB extension cable as long as it's sole purpose is the remote mounting of the key. Here's an except from the Sack Attack manual: