When connecting one of our bots to the match controller post, all the lights flash on both joystick and controller. robot-flashes red, vexnet-flashes green, game-flashes orange.
http://content.vexrobotics.com/docs/VEXnet_Cortex_UserGuide_081811.pdf (Go to page 8 of 14)
Robot red light flashing: Low/No backup battery or user microprocessor issue
VEXnet green light flashing: Linked wirelessly (no tether)
Game yellow light flashing: Disabled mode
Did you read this recent post? It goes into a lot of detail.
Do you have the 9v battery plugged in? Is that battery dead?
Can you check for bent pins on the joystick or field controller ports? Have you tried a second tower?
What firmware are you on?