This could be a few things...
Do you have the auto reset jumper installed? "a 2-pin header to the "Autoreset Enable" jumper labeled AUTO RST on the silkscreen. This is located between the Z stepper motor socket and pins 8-10 of the ATMEGA1284P socket."
This enables the serial interface to be able to reset the board to run the bootloader you installed
Do you have the auto reset jumper installed? "a 2-pin header to the "Autoreset Enable" jumper labeled AUTO RST on the silkscreen. This is located between the Z stepper motor socket and pins 8-10 of the ATMEGA1284P socket."
This enables the serial interface to be able to reset the board to run the bootloader you installed