Arduventure is using the first 16 bytes of EEPROM. This area has been reserved by the Arduboy library for system use and should not be used by sketches, so my sketch above doesn't clear it.
@DSSiege11 should modify Arduventure to only use EEPROM above EEPROM_STORAGE_SPACE_START which is defined in the Arduboy library.
Edit: This has now been done.
In the mean time, if you want to clear absolutely all of EEPROM, and thus include the area Arduventure is using, change
0 in the sketch above.