You should be able to stop Gnome overwriting your settings if you
disable its mouse plugin by navigating to
"apps/gnome_settings_daemon/plugins/mouse/" in gconf-editor and un-
ticking "active", then configure manually with a file in xorg.conf.d
(see man sysnaptics for syntax).

@Henrik:
Could you point me to the patches/source combo to compile this on other 
distros/without dkms?

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https://bugs.launchpad.net/bugs/308191

Title:
  Multitouch support not available for Synaptics touchpads v7.2

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