I did some more research and I found out that other users on my system do not have this problem. Therefore, it must be a user-specific configuration that triggers this bug.
Assuming GTK is the culprit, I tried deleting ~/.config/gtk-3.0 and this solves the problem partially. When I start xournal from the command line it now works fine. However, when I start xournal from Nautilus (by right-clicking a PDF file, open with Xournal) it still displays the abnormal toolbar. Here is the contents of ~/.config/gtk-3.0/setting.ini: [Settings] gtk-theme-name=Industrial gtk-icon-theme-name=hicolor gtk-font-name=Source Sans Pro Semi-Light 10 gtk-cursor-theme-name=crystalwhite gtk-cursor-theme-size=0 gtk-toolbar-style=GTK_TOOLBAR_BOTH gtk-toolbar-icon-size=GTK_ICON_SIZE_LARGE_TOOLBAR gtk-button-images=1 gtk-menu-images=1 gtk-enable-event-sounds=1 gtk-enable-input-feedback-sounds=1 gtk-xft-antialias=1 gtk-xft-hinting=1 gtk-xft-hintstyle=hintfull gtk-xft-rgba=rgb gtk-application-prefer-dark-theme=1
