Problem persists in 9.04.
My current work-around (for synaptics touchpad): Go to 
System->Preferences->Startup Applications and add this new command: 
xinput set-int-prop "SynPS/2 Synaptics TouchPad" 275 8 2 3 0 0 3 2 1

I think this is a bug and not a wishlist item. Of course, there are very
few left-handed people who use a left-handed mouse on a laptop. But for
those of us who do use this option, tapping on our touchpad results in a
right-click instead of a left-click. Very annoying.

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gnome-mouse-properties does not switch touchpad tap-buttons
https://bugs.launchpad.net/bugs/140574
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