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xkb settings messed up, seems to be two keyboards installed

I have two keymaps that I used to switch between with xkb alt_shift_toggle. At
some point it stopped working. xfce xkb applet shows that the keyboard is
switching but it doesn't do anything, sometimes it decides to start switching
between US and en_US instead of IL. setxkbmap does change the keyboard.

I tried fbxkb which gives the error:

xkb group #0 is already defined
kbd group numbering is not continous
run 'xlsatoms | grep pc' to know what hapends

and running that gives:
# xlsatoms | grep pc
173	pc+us
181	pc(pc105)
206	pc+us+il(lyx):2+group(alt_shift_toggle)
208	pc(pc104)
237	pc+us+inet(evdev)+group(alt_shift_toggle)

keyboard setup in xorg.conf

Section "InputDevice"
    Identifier     "Generic Keyboard"
    Driver         "kbd"
    Option         "CoreKeyboard"
    Option         "XkbRules" "xorg"
    Option         "XkbModel" "pc104"
    Option         "XkbLayout" "us,il"
    Option         "XkbVariant" ",lyx"
    Option         "XkbOptions" "grp:alt_shift_toggle"
#    Option         "XkbOptions" "grp:alt_shift_toggle"
#    Option         "XkbOptions" "grp:lwin_toggle"

I can't find anything in .xsession-errors or /var/log/Xorg.0.log

any ideas what is going on here?


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