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I found that the Crtl-Gui configuration wasn't actually being retained in EEPROM, when resetting or power cycling the board.
Doing some digging .... the keymap_config_t structure uses a WORD (16 bit value), but the EECONFIG is only allocating a byte (8 bits).
This was fun, up until now, since it was only using 8 bits. However, adding Ctrl-GUI swapping exceeded the EEPROM allocation, and was getting truncated.
This adds another range for the EECONFIG storage, and fixes the functions to properly read from and write to EEPROM.