Qt Application Disobeying Xmodmap

It seems to be Qt specific (from trying in Qt Assistant). I think it is because Qt uses only the scrolling distance for its wheel events.

Instead of using xmodmap here, you can set your scrolling distance to negative values.

You can set it through a file in /etc/X11/xorg.conf.d/, for a mouse managed by evdev :

Section "InputClass"
        Identifier "Reverse Scrolling"
        MatchIsPointer "on"
        Option "VertScrollDelta" "-1"
        Option "HorizScrollDelta" "-1"
        Option "DialDelta" "-1"
EndSection

Or you can try with xinput first :

xinput set-prop <your device id> "Evdev Scrolling Distance" -1 -1 -1

(To get the device id : xinput list)

The properties are listed with the actual device. Here xinput list-props 12 should list the properties of the touchpad. As it is a synaptics touchpad, from this man page the property should be :

xinput set-prop <touchpad id> "Synaptics Scrolling Distance" -1 -1 (Only two values, vertical and horizontal edges.)

For the rule in the configuration file, it should work with MatchIsTouchpad :

Section "InputClass"
        Identifier "Natural Scrolling"
        MatchIsTouchpad "on"
        Option "VertScrollDelta" "-1"
        Option "HorizScrollDelta" "-1"
EndSection