The problem then may occur in three ways: the program does not write correctly to the EEPROM, or it does not read correctly, or both.

You can distinguish these with writing to the EEPROM from the 'C' and reading from the 'S', and vice versa.

Then you should start to hunt down the raw cause of the problem: marginal pullup resistors and marginal timing comes into mind.

But you should really start with writing a simple "blinking LED" program and test it on both the 'C' and the 'S', as Andy recommended above. It's a fast and easy test of whether the system clock is running the same in both cases.

JW