The Smart Client remembers the opened tool windows and the layout of those opened tool windows when the Smart Client shuts down. Therefore the Smart Client is able to restore the last opened windows and their layout on start up.
If you want to return to the default windows layout i.e. the layout that was presented when you first started the Smart Client after installation you can do so by going to the Backstage Menu's Smart Client Administration Section and select Reset windows layout. After acknowledging a confirmation message layout will be reset to the default.
The windows layout is persisted in a simple XML file located in the roaming application data directory and named PersistedLayout.xml. If you delete this file the Smart Client will copy the default layout XML file from the Program Directory.