Comment 2 for bug 1201294

Some findings:

1. The bug can't be reproduced when the dialog behavior is set to 'Floating' in the preferences (Interface>Windows>Dialog behavior in 0.49), but only when the preference is set to 'Docked' and when the dialog is undocked.

2.1. When closing the dialog (X icon or Ctrl+W), Inkscape calls Inkscape::UI::Dialog::Dialog::save_geometry(), which then calls Inkscape::UI::Dialog::DockBehavior::get_position(int &x, int &y). The returned position is related to a Widget::DockItem and is not correct.
2.2. When closing the application with the dialog open, save_geometry() then calls Inkscape::UI::Dialog::FloatingBehavior::get_position(int &x, int &y). The returned position is related to a Gtk::Dialog and is correct (that's the reason why the dialog's position is correct when you restart Inkscape).