Natural scrolling using ".Xmodmap": pointer = 1 2 3 5 4 7 6 8 9 10 11 12 doesn't work anymore in 12.04 on some Ubuntu-specific apps like the Software Center, settings window, and update-center. Under what package should I report the bug?
I'm horribly late to this, but I just finished writing a guide which could help you or anyone passing by. If you still have this problem, that is.
The gist of it is that you need to get your touchpad's ID with the xinput list command, then the current scrolling distance with xinput list-props [touchpad-id] | grep "Scrolling distance". The output should be something like:
Synaptics Scrolling Distance (288): 106, 106
Here, 288 is the property ID and 106, 106 are the current values. What you need to do is invert the numbers - here, the new values will be -106, -106. This command does it:
xinput set-prop [touchpad-id] [property-id] [new-values]
I have this in a shell script set to run on login, along with commands to restart nautilus, which may or may not work for you (it's in the linked blog post).
