This is because of patch 104_always_enable_tapping.patch in xserver-
xorg-input-synaptics which hard codes the initial tapbutton values in
the source, and the values need to be different when in left handed
mode.

-    /* Enable tap if we don't have a phys left button */
-    tapButton1 = priv->has_left ? 0 : 1;
-    tapButton2 = priv->has_left ? 0 : 3;
-    tapButton3 = priv->has_left ? 0 : 2;
+    /* Enable tap */
+    tapButton1 = 1;
+    tapButton2 = 2;
+    tapButton3 = 3;

>From man synaptics --

       Button mapping for physical buttons is handled in the server.  If
the device is switched to left-handed (an in-server mapping  of physical
buttons 1, 2, 3 to the logical buttons 3, 2, 1, respectively), both
physical and TapButtons are affected. To counteract this, the TapButtons
need to be set up in reverse order (TapButton1=3, TapButton2=1).


They have added support of enabling/disabling TapButtons via input properties 
in the g-s-d mouse capplet upstream now, but perhaps an additional check for 
left handedness could be added to change how it assigns the buttons?

http://git.gnome.org/cgit/gnome-settings-
daemon/commit/?id=4eb9bd09219afbb56f114a2d10bc585e24db803e

Sorry if I'm misunderstanding the situation.

-- 
Touchpads should be unaffected by left handed mouse option
https://bugs.launchpad.net/bugs/27724
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which is subscribed to xserver-xorg-input-synaptics in ubuntu.

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