Touchpad scrolling direction reverses after sleep mode (16.04)


I am using Ubuntu MATE 16.04 LTS.

I have had trouble adjusting the scrolling direction of my touchpad.
Originally (right after installing the OS), the scrolling was reversed (so-called "natural" scrolling). I wanted the more classical option. In the "mouse preferences" window of the control panel, the "natural scrolling" box is unchecked. Checking it doesn't seem to change anything (even after reboot). Same in dconf editor.

I did some research and found this thread:

I put a .Xmodmap file containing pointer = 1 2 3 5 4 6 7 8 9 10 11 12 in my home folder.
After rebooting, it worked for a while, then the direction reversed again for no apparent reason (I now suspect it reversed after sleep mode).
I have now deleted that .Xmodmap file.

Here's the behavior that I observe:
After each reboot, I get the natural (reversed) scrolling direction.
Then, when I put the computer in sleep mode (e.g., by closing the laptop lid), and then return from sleep mode, the scrolling is now normal. If I do it once more, it doesn't reverse again (the scrolling direction stays normal).

Actually I just did some tests while writing this post and other touchpad parameters are similarly affected. If in the touchpad settings I assign "two-finger click" to "middle button", after a reboot it doesn't take effect, but after one sleep it works.

Another symptom: using evince to open a pdf, scrolling with a touchpad is supposed to be smooth. After a reboot, I get discontinuous (and reversed) scrolling, and after sleep mode I get smooth scrolling.