EEPROM is still turned on in that Configuration.h file.

#define EEPROM_SETTINGS
//to disable EEPROM Serial responses and decrease program space by ~1700 byte: comment this out:
// please keep turned on if you can.
#define EEPROM_CHITCHAT

Can you post a picture of your bed and nozzle with the probe down? I'm wondering if your probe offsets are inverted.