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.
Bug #949465 is a similar-sounding duplicate which was reported for natural scrolling in Nautilus. It's filed against the
Either that, or may want to try filing bugs against the packages for all affected windows. For example, the packages for the software you have listed above would be:
You can report bugs against any of these by running