I tried redefining the ports in "app_global.h" to match the PCIE pinout shown on the schematics:
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#define PORT_I2S_DAC0 XS1_PORT_1O // was XS1_PORT_1D
#define PORT_I2S_DAC1 XS1_PORT_1H
#define PORT_I2S_ADC0 XS1_PORT_1J // was XS1_PORT_1K
#define PORT_I2S_ADC1 XS1_PORT_1L
#define PORT_I2S_LRCLK XS1_PORT_1I
#define PORT_I2S_BCLK XS1_PORT_1K // was XS1_PORT_1A
#define PORT_MCLK_IN XS1_PORT_1E
#define PORT_GPIO XS1_PORT_4E
#define PORT_I2C XS1_PORT_8D //was XS1_PORT_4F
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#define P_GPIO_COD_RST_N 0x01
#define P_GPIO_MCLK_SEL 0x02
#define P_GPIO_SS_EN_CTRL 0x04
#define P_GPIO_LED 0x08