The EEPROM emulation uses two flash memory sectors. One is 16K and the other is 64K. The flash memory is erased to 0xff bytes, and you can only write 0 bits to individual bits. You can't set a bit back to 1 without erasing the whole sector. In order to do the EEPROM emulation, two sectors are used, and when a sector runs out of free space, all of the data is copied to the other page, then the original page is erased. It just happens that the sectors are different sizes because that's what was left over after allocating everything else. Even 16K is much bigger than the 2K EEPROM emulation because of overhead and you want to go as long as possible between sector erases to reduce wear on the flash and also processor time, as it's a lengthy operation that runs with interrupts disabled.