@deussingularis and @lamarobot :
Before I upload a new sketch I run the eeprom_clear sketch to wipe out my board then upload the new sketch to it.
I run Arduin 1.65, but also have 1.06 and 1.69
The eeprom_clear sketch is located in:
File -> Examples -> EEPROM -> eeprom_clear
I compile and load it to my board and it wipes out the existing program.
Then I open my configuration.h file and verify/change the line in the
######### misc. settings #########
section to read
#define EEPROM_MODE 1
I turned on line numbers so in mine its line 377.
Then I compile and upload it and in Repetier-Host I am able to access EEPROM configuration.
I hope that helps. It works for me.Like Repetier stated earlier only Repetier and Marlin show up in that selection.