I tested it using the attached firmware, I do not see any issue as such problem. Please refer the attached firmware to handle your GPIO signals.To test, program the img onto the FX3. The GPIO0 pin will be low here, transfer some data using the bulk out endpoint through control center, now measure the voltage on the GPIO-it should be high
Also, please make sure that the same GPIO is not be driven from the GPIF state machine as well.
Please let us know for any clarification
USBBulkLoopManual_gpiotest.zip 473.8 K