We solved this problem by adding the following code to our uEnv.txt file:

uenvcmd=i2c mw 0x24 0x01 0x2e 0x01; if run loadzimage; then run loadfdt;run 
mmcboot;fi;

The i2c command writes to the power management IC TPS65271 to disable the 
usb power before it boots Linux. If you plugin an USB cable now, the system 
boost up for one second until it executes the code in the uEnv.txt file and 
then it goes off. That is ok for our application.

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