I have the same issue on 13.10. The only key in gconf is:
graingert@flehmen:~$ cat ~/.gconf/desktop/gnome/peripherals/touchpad/%gconf.xml
<?xml version="1.0"?>
<gconf>
<entry name="config_migration_needed" mtime="1378851574" type="bool"
value="true"/>
</gconf>
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https://bugs.launchpad.net/bugs/1176389
Title:
Vertical scrolling disabled by default
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