I have been able to solve this.

The problem was the .profile file in the home directory of the userid.
the PATH variable had a reference to a symlink in /opt. The content
under the symlinked directory had 777 permissions. After changing that
to something less permissive, the problem went away.

This is my PATH variable:

PATH="$HOME/bin:$HOME/.local/bin:/opt/sub3dtool:/opt/android/sdk
/platform-tools:/opt/android-studio/bin:$PATH"

Then I set the symlinked directory permissions to 755:

gunner@minix:~$ ls -l /opt | grep sub3dtool
lrwxrwxrwx 1 root   root     16 Apr 22 10:47 sub3dtool -> sub3dtool-0.4.2/
drwxr-xr-x 4 root   root   4096 Apr 22 10:47 sub3dtool-0.4.2

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https://bugs.launchpad.net/bugs/1767670

Title:
  Menus for some apps always displayed below the app tittlebar

Status in bamf package in Ubuntu:
  New
Status in unity package in Ubuntu:
  New

Bug description:
  Description:  Ubuntu 16.04.4 LTS
  Release:      16.04

  Running 16.04 & Unity on a new Dell XPS 13 9360 laptop, freshly
  installed. The menus for some apps (terminal, nautilus) are always
  shown below the app title bar. Some other apps like Chrome or gedit do
  show correctly at the top bar as it is supposed to considering the use
  of global menus.

  This is weird as it does not happen for both userids configured on
  this machine. The other user's desktop session shows menu for all apps
  at the top bar using global menus correctly.

  See pic. And never mind the Macbuntu theme, I just installed it to
  test with it, but the same behavior was experienced before I did it.

  Also, on an external display I connect, the nautilus menus show up on
  the desktop.

  If I completely wipe this userid and recreate it, menus work as
  expected, but over time it reoccurs. I have not been able to identify
  what triggers it.

  Coincidentally, libreoffice will not even open for this user session,
  but works well for the other.

  This bug seem to show a somehow similar behavior to another reported bug in 
the sense that it only happens for one userid session and not for the other.
  see https://bugs.launchpad.net/ubuntu/+source/bamf/+bug/1532226

  I have also posted this for help in askubuntu.
  
https://askubuntu.com/questions/1028598/ubuntu-16-04-broken-menus-for-gtk-apps-always-displayed

  Can anyone help me with the commands I should run to produce a system
  report for the community to analyze it?

  Thanks.

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