If the PMODE lines are connected as PMODE[2:0] = 111, the FX3 comes up as Cypress Benicia USB Boot Device (VID: 04B4 and PID: 00BC). This doesn't work with 32-bit GPIF.
Make sure that the PMODE pins are connected as PMODE[2:0] = Z11, so that the device enumerates as Cypress FX3 Bootloader Device. This ensures the 32-GPIF functionality.
This can also happen when you connect FPGA to FX3 explorer kit using FMC Connector. FMC connector maps the PMODE pins to some other pins on the FPGA. There is a chance that the PMODE values seen by the FX3 is 111 instead of Z11.
1. Make sure that the pins of the connector mapped to PMODE lines should be removed/disconnected
2. Program FX3 first and connect FPGA