What if you do the following:

Go to Trisquel/GNOME Applications menu → System configuration → Tweak tool → Appearance

And in all the dropdown menus below theme, put the following:

- Window: Adwaita (default)
- GTK+: Adwaita (default)
- Icons: Gnome (default)
- Cursor: Adwaita (default)

Now simply try opening an application that is known to have issues. If it persists, try to log out and back in.

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