Hi Martin,
We cannot reproduce anything like this on any of our development machines (and we use exclusively Linux and FreeBSD).
Please note that we do not recommend Xfce as one of our supported graphical desktops. See our
System Requirements page. The recommended X11 configuration for PixInsight 1.8 is Fedora 19 x86_64 or later with KDE 4.8 or later, or Gnome 3.2 or later. Any modern version of Ubuntu should also work without problems. I strongly recommend you update your system to the latest Ubuntu 14 version (version 12.04 is from 2012!).
Note also that Xfce is based on GNOME 2.x (which we don't support officially) and isn't being actively developed (the latest stable version of Xfce is 4.10, released April 2012).
You can reset all PixInsight settings to default values by running it with the --uninstall argument:
$ PixInsight --uninstall
You can also make a backup copy of the configuration file:
$HOME/.PixInsight/PixInsight64.conf
which you can restore to recover all your personal settings.