I'm not surprised that an application like this does that. The manpage states
the following:
"gsynaptics, the gsynapticsis a gui for configure synaptics touchpad without
editing X configuration files."
I'm not sure what else the application would do, if it didn't override touchpad
settings.
** Changed in: gsynaptics (Ubuntu)
Status: New => Invalid
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synaptics driver disregards some xorg.conf settings
https://bugs.launchpad.net/bugs/160624
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