I found an error on line 140 in mt3620_avnet_dev.h of the reference design software.
mt3620_avnet_dev.h
line 139 /// <summary>Click Module 2 PWM is GPIO 1.</summary>
line 140 #define AVT_SK_CM2_PWM AVT_MODULE_GPIO0_PWM1
line 140 should be =>> #define AVT_SK_CM2_PWM AVT_MODULE_GPIO1_PWM1
Found some other errors in the documentation
From my testing the user LEDs are:
RED = GPIO7
GREEN = GPIO8
BLUE = GPIO9
and the APP LED = GPIO10
Scott