it would seem that something went wrong with your download of the live cd, as stepconf should work without any problems. however, here are a couple files I'm just posting the code so you can get the timings.
sample.hal
Code:
# Generated by stepconf at Tue Nov 27 19:39:22 2007
# If you make changes to this file, they will be
# overwritten when you run stepconf again
loadrt trivkins
loadrt [EMCMOT]EMCMOT base_period_nsec=[EMCMOT]BASE_PERIOD servo_period_nsec=[EMCMOT]SERVO_PERIOD traj_period_nsec=[EMCMOT]SERVO_PERIOD key=[EMCMOT]SHMEM_KEY num_joints=[TRAJ]AXES
loadrt probe_parport
loadrt hal_parport cfg=0x378
setp parport.0.reset-time 4000
loadrt stepgen step_type=0,0,0
loadrt charge_pump
addf parport.0.read base-thread
addf stepgen.make-pulses base-thread
addf charge-pump base-thread
addf parport.0.write base-thread
addf parport.0.reset base-thread
addf stepgen.capture-position servo-thread
addf motion-command-handler servo-thread
addf motion-controller servo-thread
addf stepgen.update-freq servo-thread
net xdir => parport.0.pin-02-out
net xstep => parport.0.pin-03-out
setp parport.0.pin-03-out-reset 1
net ydir => parport.0.pin-04-out
net ystep => parport.0.pin-05-out
setp parport.0.pin-05-out-reset 1
net zdir => parport.0.pin-06-out
net zstep => parport.0.pin-07-out
setp parport.0.pin-07-out-reset 1
net charge-pump => parport.0.pin-17-out
# net estop-ext <= parport.0.pin-10-in
setp stepgen.0.position-scale [AXIS_0]SCALE
setp stepgen.0.steplen 1
setp stepgen.0.stepspace 0
setp stepgen.0.dirhold 35000
setp stepgen.0.dirsetup 16000
setp stepgen.0.maxaccel [AXIS_0]STEPGEN_MAXACCEL
net xpos-cmd axis.0.motor-pos-cmd => stepgen.0.position-cmd
net xpos-fb stepgen.0.position-fb => axis.0.motor-pos-fb
net xstep <= stepgen.0.step
net xdir <= stepgen.0.dir
net xenable axis.0.amp-enable-out => stepgen.0.enable
setp stepgen.1.position-scale [AXIS_1]SCALE
setp stepgen.1.steplen 1
setp stepgen.1.stepspace 0
setp stepgen.1.dirhold 35000
setp stepgen.1.dirsetup 16000
setp stepgen.1.maxaccel [AXIS_1]STEPGEN_MAXACCEL
net ypos-cmd axis.1.motor-pos-cmd => stepgen.1.position-cmd
net ypos-fb stepgen.1.position-fb => axis.1.motor-pos-fb
net ystep <= stepgen.1.step
net ydir <= stepgen.1.dir
net yenable axis.1.amp-enable-out => stepgen.1.enable
setp stepgen.2.position-scale [AXIS_2]SCALE
setp stepgen.2.steplen 1
setp stepgen.2.stepspace 0
setp stepgen.2.dirhold 35000
setp stepgen.2.dirsetup 16000
setp stepgen.2.maxaccel [AXIS_2]STEPGEN_MAXACCEL
net zpos-cmd axis.2.motor-pos-cmd => stepgen.2.position-cmd
net zpos-fb stepgen.2.position-fb => axis.2.motor-pos-fb
net zstep <= stepgen.2.step
net zdir <= stepgen.2.dir
net zenable axis.2.amp-enable-out => stepgen.2.enable
net estop-out <= parport.0.pin-10-in-not
net estop-out => iocontrol.0.emc-enable-in
loadusr -W hal_manualtoolchange
net tool-change iocontrol.0.tool-change => hal_manualtoolchange.change
net tool-changed iocontrol.0.tool-changed <= hal_manualtoolchange.changed
net tool-number iocontrol.0.tool-prep-number => hal_manualtoolchange.number
net tool-prepare-loopback iocontrol.0.tool-prepare => iocontrol.0.tool-prepared
sample.ini
Code:
# Generated by stepconf at Tue Nov 27 19:39:22 2007
# If you make changes to this file, they will be
# overwritten when you run stepconf again
[EMC]
MACHINE = my-mill
NML_FILE = emc.nml
DEBUG = 0
[DISPLAY]
DISPLAY = axis
POSITION_OFFSET = RELATIVE
POSITION_FEEDBACK = ACTUAL
MAX_FEED_OVERRIDE = 1.2
INTRO_GRAPHIC = emc2.gif
INTRO_TIME = 5
PROGRAM_PREFIX = /home/ubuntu/emc2/nc_files
INCREMENTS = .1in .05in .01in .005in .001in .0005in .0001in
[TASK]
TASK = milltask
CYCLE_TIME = 0.010
[RS274NGC]
PARAMETER_FILE = emc.var
[EMCMOT]
EMCMOT = motmod
SHMEM_KEY = 111
COMM_TIMEOUT = 1.0
COMM_WAIT = 0.010
BASE_PERIOD = 24500
SERVO_PERIOD = 1000000
[HAL]
HALFILE = my-mill.hal
HALFILE = joypad.hal
[TRAJ]
AXES = 3
COORDINATES = X Y Z
LINEAR_UNITS = inch
ANGULAR_UNITS = degree
CYCLE_TIME = 0.010
DEFAULT_VELOCITY = 0.10
MAX_LINEAR_VELOCITY = 1.02
[EMCIO]
EMCIO = io
CYCLE_TIME = 0.100
TOOL_TABLE = tool.tbl
[AXIS_0]
TYPE = LINEAR
HOME = 0.0
MAX_VELOCITY = 1.02040816327
MAX_ACCELERATION = 20.0
STEPGEN_MAXACCEL = 21.0
SCALE = 40000.0
FERROR = 0.05
MIN_FERROR = 0.01
MIN_LIMIT = -400.0
MAX_LIMIT = 90000000000.0
HOME_OFFSET = 0.0
[AXIS_1]
TYPE = LINEAR
HOME = 0.0
MAX_VELOCITY = 1.02040816327
MAX_ACCELERATION = 20.0
STEPGEN_MAXACCEL = 21.0
SCALE = 40000.0
FERROR = 0.05
MIN_FERROR = 0.01
MIN_LIMIT = -400.0
MAX_LIMIT = 90000000000.0
HOME_OFFSET = 0.0
[AXIS_2]
TYPE = LINEAR
HOME = 0.0
MAX_VELOCITY = 1.0
MAX_ACCELERATION = 30.0
STEPGEN_MAXACCEL = 31.5
SCALE = 8000.0
FERROR = 0.05
MIN_FERROR = 0.01
MIN_LIMIT = -4.0
MAX_LIMIT = 99999999.0
HOME_OFFSET = 0.0
In stepconf, the preset timings for the Gecko is
step time: 4000ns
step space: 500ns
Direction hold: 20000ns
direction setup: 1000ns
hope that helps. I'd supply better .hal and .ini files, but i'm just getting things setup myself.