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I have tried this component with the same result. There is still a warning with your component during initializing, I have used Creator 4.2.
I have the project attached, please have a look.
I also think it is about timing, I use USB HID report with 64 Bytes, but I have increased the interval already to the maximum of 255 ms.
If I use the EEPROM in separate projects, it works fine.
I think I basically need something like:
If EEPROM data needs to be written, stop(halt) everything and do only the EEPROM function, then when finish, continue with the rest as usual. If I lost some USB transfers, that would be acceptable. The EEPROM function need to be only executed, if new(different) data available for the EEPROM.
I am no looking into the topic interrupts to see if I can solve the problem that way.