Yeah, I think it's a timer problem, as said above. The code begins executing as soon as the robot controller gets contact with the OI. The master processor just doesn't allow anything to be output to the speed controllers. Your timer is probabaly expiring before your robot gets a chance to do anything.
If you look at
Team Update 11 it shows how the bits are for the phases of the match. Whenever autonomous mode is set to 1, all operator interface feedback will be overridden.
When comp_mode is 0, your robot is active. Basically, make your if statements to read:
If auton_mode = 0 or comp_mode = 1 or rc_sw14 = 0 then skip_Blah