Reverse scrolling in some applications

[Bleznudd]

Hi everyone,
Since a couple of days I have a really strange sort of bug. In some applications (Spotify and libreoffice) the natural two finger scroll have becomed standard scroll; if in every other application I scroll up and the page goes down, in this two if I scroll up the page also go up.
I have to say that all was working properly before the last update, then touchpad settings disappeared and the scroll became standard. I fixed it creating the 50-synaptics.conf file and putting in this

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Option "VertScrollDelta" "-111" This solution worked for almost every application except for spotify and libreoffice. Why? Is there a solution?

I'm on Manjaro 15.12 64-bit
DE: Budgie (but this also happen when i run Gnome)
Kernel: 4.4.8-1 (but this also happen with 4.1 and 4.5)
My touchpad in an Alps touchpad
xinput output:

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⎡ Virtual core pointer                    id=2 [master pointer  (3)]
⎜   ↳ Virtual core XTEST pointer              id=4 [slave  pointer  (2)]
⎜   ↳ touchpad                                id=6 [slave  pointer  (2)]
⎣ Virtual core keyboard                    id=3 [master keyboard (2)]
    ↳ Virtual core XTEST keyboard              id=5 [slave  keyboard (3)]
    ↳ Power Button                            id=7 [slave  keyboard (3)]
    ↳ Video Bus                                id=8 [slave  keyboard (3)]
    ↳ Power Button                            id=9 [slave  keyboard (3)]
    ↳ HP Truevision HD                        id=10 [slave  keyboard (3)]
    ↳ AT Translated Set 2 keyboard            id=11 [slave  keyboard (3)]
    ↳ HP Wireless hotkeys                      id=12 [slave  keyboard (3)]
    ↳ HP WMI hotkeys                          id=13 [slave  keyboard (3)]
Thanks

[c00ter]

I don't know if this has anything  to do with it, but the GNOME/GTK3 3.20 update changed the touchpad driver to libinput, and did away with synaptics. It also instituted several changes to touchpad settings. So you might compare the update touchpad change announcement, your installed drivers, and the new settings.

Reference: https://bbs.archlinux.org/viewtopic.php?id=211328

Regards

[Bleznudd]

Thanks for the answer, I've tried removing my 50-synaptics.conf file ad installing xf86-input-libinput  0.15.0-1, this restored my mouse and touchpad setting, but my touchpad became unsable because of the extreme sensibility even at the lowest speed. And most important it hasn't resolved the problem with Spotify ad libreoffice. So I have removed xf86-input-libinput and returned to synaptics and noticed that this problem also occur when I'm using the mouse.
This is really frustrating especially when using epiphany and libreoffice at the same time, one of them with natural scroll and the other one with standard scroll.
Any other ideas ?

Maybe downgrading to GNOME/GTK 3.18 ? If yes, how can I do it?

Thanks

[c00ter]

Did you remove the xf86-input-synaptics driver? If you install xf86-input-libinput, you also have to remove it, as well as the synaptics config file.

Rather than downgrade, if this issue recurs after making those changes & re-booting, I would see if the GNOME shell touchpad extension offered any relief.

Regards