I suppose you are loading the CyBootProgrammer firmware in the I2C EEPROM, correct? And the you are trying to boot from I2C.
First can you verify that the I2C read/write is proper? You can do so, by programming the USBFlashProg example in the FX3 RAM. Please refer to the readme of the project to know the vendor command to read and write from the I2C. Try to perform a write and read operation and verify if the data is being correcly written and read back.
Also, try to monitor the I2C communication signals, and check if somehow the SDA/SCLK is pulled low. Is it your own custom board, do you have multiple I2C masters?
If you have a CYUSB3KIT-003 EZ-USB® FX3™ SuperSpeed Explorer kit, it is best to test.