Hello, everyone.
Can I get advices about the accidents I had with Antergos + Openbox?

On March 18, 2016, I did “sudo pacman -Syu” on my Antergos (the preconfigured Openbox version.) I saw no error messages from terminal emulator and pacman. However, the next morning I found a very plain Openbox desktop, just like Antergos’ fresh installation result.

My ~/.xinitrc and ~/.config/openbox/autostart were overwritten by someone. The config files timestamps are March 18.
Thus all my personal configurations including wallpaper, openbox menu, conky, icons theme, window theme, cursor theme, desktop font setup, are lost.
Graphically speaking, it looks like this now:
alt text (for full sized image, https://someimage.com/v0sfVg)

And it is supposed to be like this:
alt text
(for full sized image, https://someimage.com/LB3nEIj)

My pacman.log is browsable here:
http://pastebin.com/gj4dTGa5

My pamac.log is browsable here:
http://pastebin.com/8nL5Ufvg

To be open, I fresh-installed this Antergos Openbox system in November 2015. And this is my second experience of config loss after pacman -Syu. The first incident happened in middle of January, i.e., two months ago.
I guess the following part of my pacman.log is telling me something.

[2015-12-13 20:04] [ALPM] upgraded openbox (3.6.1-1 -> 3.6.1-2)

[2016-01-18 20:41] [ALPM] upgraded antergos-openbox-setup (0.2.5-1 -> 0.2.6-3) 
[2016-01-18 20:41] [ALPM-SCRIPTLET] Setting Antergos Openbox setup to user harry [
[2016-01-18 20:45] [ALPM] upgraded openbox-menu (0.7.0-2 -> 0.8.0-1)

[2016-03-18 23:49] [ALPM] upgraded openbox (3.6.1-2 -> 3.6.1-3)
[2016-03-18 23:50] [ALPM] upgraded antergos-openbox-setup (0.2.6-3 -> 0.2.7-1)
[2016-03-18 23:50] [ALPM-SCRIPTLET] Setting Antergos Openbox setup to user harry
[2016-03-18 23:49] [ALPM] upgraded openbox (3.6.1-2 -> 3.6.1-3)

Thank goodness, my /etc/fstab and (surprisingly) my Japanese Input Method survived. (Fcitx-Mozc)

So, am I doing something wrong? Any advice would be appreciated.
For your information, my pacman.conf holds [antergos] repository.
Maybe I should comment out this repo entry?
Or should I switch to Xfce or DE something?
(I have also installed Antergos-GNOME into another more powerful hardware in December 2015. So far I never experienced this kind of system update issues on the Antergos-GNOME system.)

Before I forget, the problems happen on my Lenovo ThinkPad R61 laptop, physical machine.
Thank you for your kind advices in advance.