I just hit this bug too and can confirm it for 17.10 and 18.04.

However, there is an easy workaround: Make sure Neo2 is the only layout
in your XKB keymap. The easiest way would be to have just one layout.
Another solution for me is to have exactly 4 layouts and Neo2 is the
4th. Checking with "xkbcomp $DISPLAY output.xkb" both ways lead to the
same keymap.

I will attach a working and non working xkbcomp output. Maybe someone
with more experience can diff these and find the root cause.

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https://bugs.launchpad.net/bugs/879838

Title:
  Keyboard Layout "Germany Neo 2": Mod4 does not work if used as
  secondary keyboard layout

Status in xkeyboard-config package in Ubuntu:
  Confirmed

Bug description:
  If Neo 2 is used as secondary keyboard layout, Layer 4 and 6 (that is,
  Mod4) don't work. To reproduce this bug, do the following:

  1: Neo 2 as primary keyboard layout
  - start gnome-keyboard-properties
  - Click "Add..."
  - Select Country: "Germany" and Variants: "Germany Neo 2"
  - Select "Germany Neo 2" and move it to the top of the list.
  Try to use Neo Layer 4 or 6. E.g. type the number "4" which is "Mod4" and "n" 
in Neo ("<" and "j" in standard German QWERTZ layout) or move the cursor left 
using "Mod4" and "i" ("AltGr" and "s" in QWERTZ layot).  Works as expected.

  2: Neo as secondary layout
  - Now add "Germany Eliminate dead keys" to the list and move it to the top
  - Use "Neo 2" as secondary layout
  - Click "Options" and select "Scroll lock" (or any other) as "Key(s) to 
change layout"
  Now switch to Neo using the selected key and try to type "4" or move the 
curser as above. Instead of Neo Layer 4 or 6 you will have Layer 1/3 (that is, 
you will be typing an "n" instead of a "4" and an "i" instead of moving the 
cursor left). 

  Choosing other keys for layout change or turning the compose key
  on/off does not change anything. Neither does applying "Neo 2" as
  primary layout system wide and using "Germany Eliminate dead keys"
  with "Neo 2" as a secondary keyboard layout as local user.

  Applying the patch suggested on neo-layout.org for a similar problem
  (http://wiki.neo-layout.org/ticket/174) does not have any effect.

  Description:  Ubuntu 11.04
  Release:      11.04
  xkb-data: 2.1-1ubuntu3

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