It's HOME_SEQUENCE that needs setting up.
edit: pulling from memory, so best you find the relevant bit in the documentation, but here are the joints for mine (0 and 1 are the gantry).
Code:
[AXIS_X]
MIN_LIMIT = -90
MAX_LIMIT = 1000
# set to double the value in the corresponding joint
MAX_VELOCITY = 500.0
# set to double the value in the corresponding joint
MAX_ACCELERATION = 2000.0
# shares the above two equally between the joint and the offset
OFFSET_AV_RATIO = 0.5
[AXIS_Y]
MIN_LIMIT = -90
MAX_LIMIT = 760
# set to double the value in the corresponding joint
MAX_VELOCITY = 500.0
# set to double the value in the corresponding joint
MAX_ACCELERATION = 2000.0
# shares the above two equally between the joint and the offset
OFFSET_AV_RATIO = 0.5
[AXIS_Z]
MIN_LIMIT = -94
#reduced from -100
MAX_LIMIT = 10
# set to double the value in the corresponding joint
MAX_VELOCITY = 200.0
# set to double the value in the corresponding joint
MAX_ACCELERATION = 2000.0
# shares the above two equally between the joint and the offset
OFFSET_AV_RATIO = 0.5
[JOINT_0]
AXIS = X
MIN_LIMIT = -90
MAX_LIMIT = 1000
MAX_VELOCITY = 250
MAX_ACCELERATION = 1000
TYPE = LINEAR
SCALE = 50.929581789
STEPGEN_MAX_VEL = 300.0
STEPGEN_MAX_ACC = 2400.0
FERROR = 0.05
MIN_FERROR = 0.01
DIRSETUP = 20000
DIRHOLD = 20000
STEPLEN = 5000
STEPSPACE = 5000
DEADBAND = 0
P = 1000
I = 0
D = 0
FF0 = 0
FF1 = 1
FF2 = 0.00013
BIAS = 0
MAX_OUTPUT = 0
MAX_ERROR = 0.0127
HOME = 0
HOME_OFFSET = -100
HOME_SEARCH_VEL = -100
HOME_LATCH_VEL = -10
HOME_SEQUENCE = -1
HOME_USE_INDEX = False
HOME_IGNORE_LIMITS = True
[JOINT_1]
AXIS = X
MIN_LIMIT = -90
MAX_LIMIT = 1000
MAX_VELOCITY = 250
MAX_ACCELERATION = 1000
TYPE = LINEAR
SCALE = 50.929581789
STEPGEN_MAX_VEL = 300.0
STEPGEN_MAX_ACC = 2400.0
FERROR = 0.05
MIN_FERROR = 0.01
DIRSETUP = 20000
DIRHOLD = 20000
STEPLEN = 5000
STEPSPACE = 5000
DEADBAND = 0
P = 1000
I = 0
D = 0
FF0 = 0
FF1 = 1
FF2 = 0.00013
BIAS = 0
MAX_OUTPUT = 0
MAX_ERROR = 0.0127
HOME = 0
HOME_OFFSET = -100
HOME_SEARCH_VEL = -100
HOME_LATCH_VEL = -10
HOME_SEQUENCE = -1
HOME_USE_INDEX = False
HOME_IGNORE_LIMITS = True
[JOINT_2]
AXIS = Y
MIN_LIMIT = -90
MAX_LIMIT = 760
MAX_VELOCITY = 250
MAX_ACCELERATION = 1000
TYPE = LINEAR
SCALE = 50.929581789
STEPGEN_MAX_VEL = 300.0
STEPGEN_MAX_ACC = 2400.0
FERROR = 0.05
MIN_FERROR = 0.01
DIRSETUP = 20000
DIRHOLD = 20000
STEPLEN = 5000
STEPSPACE = 5000
DEADBAND = 0
P = 1000
I = 0
D = 0
FF0 = 0
FF1 = 1
FF2 = 0.00013
BIAS = 0
MAX_OUTPUT = 0
MAX_ERROR = 0.0127
HOME = 0
HOME_OFFSET = -100
HOME_SEARCH_VEL = -100
HOME_LATCH_VEL = -10
HOME_SEQUENCE = 1
HOME_USE_INDEX = False
HOME_IGNORE_LIMITS = True
[JOINT_3]
AXIS = Z
MIN_LIMIT = -94
MAX_LIMIT = 10
MAX_VELOCITY = 100
MAX_ACCELERATION = 1000
TYPE = LINEAR
SCALE = 400
STEPGEN_MAX_VEL = 120.0
STEPGEN_MAX_ACC = 1200.0
FERROR = 1
MIN_FERROR = 1
DIRSETUP = 20000
DIRHOLD = 20000
STEPLEN = 5000
STEPSPACE = 5000
DEADBAND = 0
P = 1000
I = 0
D = 0
FF0 = 0
FF1 = 1
FF2 = 0.00013
BIAS = 0
MAX_OUTPUT = 0
MAX_ERROR = 0.0127
HOME = 0
HOME_OFFSET = 20
HOME_SEARCH_VEL = 100
HOME_LATCH_VEL = 10
HOME_SEQUENCE = 0
HOME_USE_INDEX = False
HOME_IGNORE_LIMITS = True
