This one bugs me.
I fashioned this handy script to swap the left and right mouse buttons over: [My mouse is a Razer]
/usr/bin/xinput set-button-map `xinput list | grep 'Razer' | grep -o \=[0-9]* | grep -o [0-9]*$` 3 2 1 4 5 6 7 8 1 10 11 12 13
When I run this in a Terminal it works.
When I go to Startup Application Preferences -> Add and then literally paste the above into the command field as an 'Additional startup program' It does not run on startup.
I'm using Ubuntu 11-10 but this also applied to the 10-10