I'm using Ubuntu 12.04LTS 32 bit.
I customised the /usr/share/X11/xkb/symbols/fr keyboard layout file and am using two different variants from the same file - French(alternative) and French (alternative, latin-9 only).
Until the end of June, I had a problem with these layouts being "lost" on shutdown, but there was a workaround by using this command:
setxkbmap "fr(oss)","fr(oss_latin9)"
on startup.
I was away and didn't use my pc for a month and when I came back and installed all updates (310 of them) there's a new problem. As before the keyboard layouts return to the standard non customised versions of the keyboard layouts. (I wonder where is it loading it from. Is there a backup copy somewhere?) However, if I select "Show layout chart" it does show the correct layout.
Since the updates, using the above command no longer works. The only workaround I found was to enter in the Keyboard layout settings, remove one keyboard layout and add it again. Then both layouts work perfectly.
I've attached the custom layout file.
It seems that one of the updates made changes to the keyboard layout management and now the setxkbmap workaround is no longer necessary. I had set it up as a startup command. After I disabled this command the keyboard layouts are being respected and function as desired.
Therefore this is no longer a bug.