The boot process can only load internal CY7C68013 memory from the records contained in the I2C EEPROM. Is it possible that your hex file contains records outside of that area? Note that when you download the hex file from the control panel that the external memory will be also be loaded. This is not the case when it is loaded from the I2C EEPROM.

Your program may work perfectly when you download the hex file but this is at a stage when all the USB enumeration has already been completed by the CY7C68013. With 0xC2 at the first location in the EEPROM, it is now the responsibility of YOUR code to provide all this information. This would not have been used in your “executing perfectly” test. Is this implemented in your code?

Are you sure that your code is making its way to the EEPROM correctly? Note that the Control Panel has two buttons for loading to “small” and “large” EEPROMs. I’m not sure that a verify is performed as part of this process.