<font face="Arial, Verdana">Are you using latest 0.92 version? I remember there was a problem with one mirrored motor, just not what exactly. As you see in this code</font>
<font face="Arial, Verdana"> inline void startXStep()</font>
<font face="Arial, Verdana"> {</font>
<font face="Arial, Verdana">#if !(GANTRY)</font>
<font face="Arial, Verdana"> WRITE(X_STEP_PIN,HIGH);</font>
<font face="Arial, Verdana">#if FEATURE_TWO_XSTEPPER</font>
<font face="Arial, Verdana"> WRITE(X2_STEP_PIN,HIGH);</font>
<font face="Arial, Verdana">#endif</font>
which is used to set a step there are always both set. Same in
static INLINE void endXYZSteps()
{
WRITE(X_STEP_PIN,LOW);
#if FEATURE_TWO_XSTEPPER
WRITE(X2_STEP_PIN,LOW);
#endif
WRITE(Y_STEP_PIN,LOW);
#if FEATURE_TWO_YSTEPPER
WRITE(Y2_STEP_PIN,LOW);
#endif
WRITE(Z_STEP_PIN,LOW);
#if FEATURE_TWO_ZSTEPPER
WRITE(Z2_STEP_PIN,LOW);
#endif
}
and since they have power this should work especially if it works form lcd. To make it not work you would need to make the stepper signal a input.
sd problem is not solvable if it is interference with udoo board I guess. In that case you would need to use the server software instead. After all you combine it to not use the sd card.