Hello Bence,
Based on my understanding from the latest project that was shared, you are making use of a 16 bit data bus. As mentioned in the pin description section of FX3 datasheet, GPIO 20 and 25 are used for the control signals and they cannot be directly configured over the IO matrix. You can override and use them. Please note that the API CyU3PDeviceConfigureIOMatrix () will fail if you configure one IO that is actually mapped to a peripheral as a GPIO. The control signals are mapped to the GPIF II block and it is not possible to directly configure them as GPIOs through the IO matrix configurations.
About the PWM issue, we used the same project that was shared in your previous response without any modification. We were able to see a PWM on GPIO 34. Please find the snapshot of the traces captured at our end using saleae logic analyzer:
I found that you have used a very small period for the PWM signal. Is this the actual requirement? If not then you can refer to the following KBA to understand how to calculate and set the period and duty cycle of the PWM signal:
