Please refer to section 5.1 of AN76405. This section mentions the supported EEPROM device sizes for FX3. The link to the same is given below:
From the above document, an EEPROM of 4Mbit is not supported by FX3. Please try reducing the size of .img's by building the projects in release mode and then use a 2Mbit EEPROM. We use a 2Mbit EEPROM (M24M02 from ST Electronics) for CYUSB3KIT-003.