I could reproduce a bug probably in avrdude.
Get an arduino MEGA 2560 Get Arduino IDE Get Repetier firmware with your parameters, but EEPROM_MODE 1 Upload : after 4 #, the upload hangs
Windows is messed up : zombie avrdude locks the COM port.
Edit configuration.h : EEPROM_MODE 0
Upload again : it's OK.
This happens in both Windows and Linux.
I spent 2 days on this one !