I am using the version from your github repo which I have forked. I noticed you had indeed updated the setxkb.sh script in the meantime, so I have now merged in the latest.

Here is what I observe:
In the system text entry settings, I have "English(Colemak[eD],Curl-DvbgHm ergo)". However this is effectively overridden by the setxb.sh script, which defines my custom mappings. I call this script on startup, and it works fine... until...

When I plug in the headset, I notice the following changes:
- The basic layout remains on Curl-DvbgHm but my AltGr/Extend layers are different and these revert back to the defaults.
- I have some keycode remappings in keycodes/evdev which are also lost.

I suppose this is not really a problem with your scripts, but rather an issue with Ubuntu itself: why does it feel the need to change anything related to keyboard settings whenever a USB device is plugged in? I think what is happening is it reverts back to the basic config selected in the "Text Entry" settings, so anything set with the script is lost.

I do have a suggestion though: probably there is no need to include the xkb-backup-2016-01-02 directory in the repository? It makes is awkward to deal with as after installation git thinks these are changed source files.

Please state your OS and desktop environment.

I have a different physical layout - a bluetooth apple keyboard, and that seems to get my computer tied in knots when trying to flip between the laptop and the remote keyboard.  To the point I've given up on it.  (Debian 7.9, Xfce 4.8.)  But perhaps that's a whole other can of worms to do with bluetooth or difference in physical layout.

I used to have a keyboard changer icon and multiple layouts setup under Xfce, but occasionally it would crap out, and I'd find myself in another layout.  So in the end I just reduced the list to one, shame because when I was really procrastinating I might give Colemak a whirl.

It's irritating when my partner wants to just hop on the laptop, and I have no Qwerty.  I _think_ it works okay under Debian 8.  I should investigate further.  There seems to be little issues under each and every new release and even some regression at times.  I get confused as to which setting is doing what.

By the way, pinkyache, you are a dvorak typer, right? Are you playing with Colemak nonetheless ? ;-)

I use a "grand child" of Dvorak... that is, if Dvorak were the grandmother, (stock) AdNW is its daughter and I am using an AdNW-version I made for the Dutch language.... To my fingers, for Dutch (!),
Querty is worse
Colemak is much better
Dvorak is even better
Stock AdNW (hieao) is very good
Dutch AdNW (saeio) is the best

I just open a terminal and type setxkbmap -layout nl  and I'm done. Back to normal? setxkbmap -layout us