When you start an explorer, you are looking at it in a sliding pane; the pane that the explorer displays in has slid over a portion of the Work pane. If you click an object or project tab in the Work pane, the explorer will slide back and you will have to click an explorer button to get it back.
When you click the Pushpin icon and dock the explorer, you are looking at a docked pane that is now sharing the main window space with the Work pane.
If you close Rational Synergy, then start a new session, the four explorers will display in the same order. Synergy will remember your settings and display the explorers appropriately.