A fix without using gpointing-device-settings:
First, type "xinput" in terminal. It will list your input devices. You should 
see something like this:
⎡ Virtual core pointer                          id=2    [master pointer  (3)]
⎜   ↳ Virtual core XTEST pointer                id=4    [slave  pointer  (2)]
⎜   ↳ Genius       Optical Mouse                id=8    [slave  pointer  (2)]
⎣ Virtual core keyboard                         id=3    [master keyboard (2)]
    ↳ Virtual core XTEST keyboard               id=5    [slave  keyboard (3)]
    ↳ Power Button                              id=6    [slave  keyboard (3)]
    ↳ Power Button                              id=7    [slave  keyboard (3)]
    ↳ AT Translated Set 2 keyboard              id=9    [slave  keyboard (3)]
In my case, Genius Optical Mouse is my mouse, its id is 8.
Then, type "xinput list-props <your mouse device id> | grep "Evdev Middle 
Button". You will get something like this:
        Evdev Middle Button Emulation (259):    0
        Evdev Middle Button Timeout (260):      50
The id in my case, the id of "Evdev Middle Button Emulation" is 256
Then, type "xinput set-int-prop <your mouse device id> <id of Evdev Middle 
Button Emulation> 8 1"
In my case, I should type "xinput set-int-prop 8 259 8 1"
BONUS: you can set the timeout with "xinput set-int-prop <your mouse device id> 
<id of Evdev Middle Button Timeout> 32 <timeout>"

If it works, then add "xinput set-int-prop <your mouse device id> <id of
Evdev Middle Button Emulation> 8 1" to your session startup application.
Please refer to
https://help.ubuntu.com/community/AddingProgramToSessionStartup

Hope this helps. :)

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https://bugs.launchpad.net/bugs/489830

Title:
  Settings of gpointing-device-settings are non-persistent

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