#define EXT0_TEMPSENSOR_TYPE 100

#define BEEPER_PIN 61 // Beeper on AUX-4

#define SDSUPPORT false

#define EXT0_TEMPSENSOR_PIN TEMP_0_PIN

#define ENDSTOP_Z_MIN_INVERTING true

I use a Ultimaker v1.5.7 Motherboard. I have configured it in the online configurator and made no further changes by hand. My entry in the configuration.h is #define MOTHERBOARD 37

#define DEBUG_QUEUE_MOVE

* #define STEPPER_HIGH_DELAY 0

#define KNOWN_BOARD 1

#define DELTASEGMENTS_PER_PRINTLINE 24

Maybe a speed problem. You have DOUBLE_STEP_DELAY 1000 so with double stepping your max. frequency is 1000. So you have to hope that you never reach that,#define STEPPER_HIGH_DELAY 20 is also long but

#define DELTASEGMENTS_PER_PRINTLINE 24#define STEPPER_INACTIVE_TIME 360L#define MAX_INACTIVE_TIME 360L#define MAX_FEEDRATE_X 30#define MAX_FEEDRATE_Y 30#define MAX_FEEDRATE_Z 20#define ENABLE_BACKLASH

#define DRIVE_SYSTEM 0

#define UI_ENCODER_SPEED 1

#define EXT0_ENABLE_ON 0

 #define EEPROM_MODE 1

#define EXT0_ENABLE_PIN E0_ENABLE_PIN

#define KNOWN_BOARD

or #define  FEATURE_CONTROLLER 0 all works.

#define EXT0_MAX_FEEDRATE 30