In  the display setting of the ini file you can use the GEOMETRY setting 
to make axis backplot correct for your machine.

http://www.linuxcnc.org/docs/2.3/html/config_ini_config.html#sub:%5BDISPLAY%5D-section

GEOMETRY = XYZABCUVW
    Controls the preview and backplot of rotary motion. This item
    consists of a sequence of axis letters, optionally preceded by a "-"
    sign. Only axes defined in [TRAJ]AXES should be used. This sequence
    specifies the order in which the effect of each axis is applied,
    with a "-" inverting the sense of the rotation or translation.
    The proper GEOMETRY string depends on the machine configuration and
    the kinematics used to control it. The example string
    GEOMETRY=XYZBCUVW is for a 5-axis machine where kinematics causes
    UVW to move in the coordinate system of the tool and XYZ to move in
    the coordinate system of the material. The order of the letters is
    important, because it expresses the order in which the different
    transformations are applied




Andy Pugh wrote:
> 2009/7/8 Jim Wilkin <[email protected]>:
>
>   
>> Just got my a axis going and noticed that the Axis plot screen doesn't
>> show the A axis.
>>     
>
> I noticed the same thing, but decided it was probably deliberate, as I
> can't imagine how you would show the A axis movement without knowing
> the absolute position and direction of the centre of rotation of A
> relative to the other axes.
>
>   
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