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?
https://vexforum.com/t/field-control-a-technical-analysis/25651/1
Can you check for bent pins on the joystick or field controller ports? Have you tried a second tower?
What firmware are you on?