Custom trackpad mapping doesn't work for all applications

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http://askubuntu.com – I found out I could invert my trackpad scrolling, so as to work more like the OS X "natural scrolling", which I liked better. To do that, I run the following command on startup: xinput set-button-map 11 1 2 3 5 4 7 6 Where 11 is the touchpad id (found with xinput list and xinput test 11). This inverts the vertical and horizontal two-finger scrolling, and works fine in Terminal, Chrome, Document Viewer, etc. However, it doesn't work in Nautilus and some applications such as the Update Manager, as they keep the usual mapping. I'm running Ubuntu 12.04 x64 Why does this mapping work for some (HowTos)