I've found a similar thing; the only option that I've seen affected is
HorizEdgeScroll, which is off by default but turned on in my xorg.conf
file. If I enable SHMConfig I can use synclient to turn it on and it
works fine, but simply setting it in the config file doesn't work. It
looks like it does, the X log shows it being turned on, but it doesn't
get turned on or doesn't stay on. Can't blame it on gsynaptics with
SHMConfig turned off. So I assume that either it isn't getting set or
something else is turning it off, but I can't figure out what.

Certainly not a major problem, just need to remember to run synclient
when logging in after an X server restart.

Here's the relevant part of /etc/X11/xorg.conf:
Section "InputDevice"
        Identifier      "Synaptics Touchpad"
        Driver          "synaptics"
        Option          "SendCoreEvents"        "true"
        Option          "Device"                "/dev/psaux"
        Option          "Protocol"              "auto-dev"
        Option          "LeftEdge"              "128"
        Option          "RightEdge"             "896"
        Option          "TopEdge"               "128"
        Option          "BottomEdge"            "640"
#       Option          "SHMConfig"             "true"
        Option          "SHMConfig"             "false"
        Option          "VertScrollDelta"       "12"
        Option          "HorizScrollDelta"      "16"
        Option          "VertEdgeScroll"        "true"
        Option          "HorizEdgeScroll"       "true"
#       Option          "LTCornerButton"        "0"
#       Option          "LBCornerButton"        "1"
#       Option          "RTCornerButton"        "2"
#       Option          "RBCornerButton"        "3"
EndSection

And the relevant section of /var/log/Xorg.0.log:
(II) Synaptics touchpad driver version 0.14.6 (1406)
(--) Synaptics Touchpad auto-dev sets device to /dev/input/event4
(**) Option "Device" "/dev/input/event4"
(**) Option "SHMConfig" "false"
(**) Option "LeftEdge" "128"
(**) Option "RightEdge" "896"
(**) Option "TopEdge" "128"
(**) Option "BottomEdge" "640"
(**) Option "VertScrollDelta" "12"
(**) Option "HorizScrollDelta" "16"
(**) Option "VertEdgeScroll" "true"
(**) Option "HorizEdgeScroll" "true"
(--) Synaptics Touchpad touchpad found
(**) Option "SendCoreEvents" "true"
(**) Synaptics Touchpad: always reports core events
(II) XINPUT: Adding extended input device "Synaptics Touchpad" (type: MOUSE)
(II) XINPUT: Adding extended input device "Configured Mouse" (type: MOUSE)
(II) XINPUT: Adding extended input device "Generic Keyboard" (type: KEYBOARD)
Synaptics DeviceInit called
SynapticsCtrl called.
(II) Configured Mouse: ps2EnableDataReporting: succeeded
Synaptics DeviceOn called
(--) Synaptics Touchpad auto-dev sets device to /dev/input/event4
(**) Option "Device" "/dev/input/event4"
(--) Synaptics Touchpad touchpad found

-- 
synaptics driver disregards some xorg.conf settings
https://bugs.launchpad.net/bugs/160624
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