Since it only happens in a given Autonomous mode, I would assume this is a code issue. In a regular match (during Teleoperated), do you change the state of the PCM in any way similar to your High Goal auton?
It sounds to me like 1 of 3 things:
a) Your compressor is faulty and/or not connected.
b) Your CAN bus is not connected properly to the PCM
c) Your CAN bus is being over utilized. Check the Driver Station Logs for CAN % utilization.
A and B both come from the
CTRE PCM Users Manual