I Tested the latest build, to reproduce the problem,
1) run the sample TestApp,
2) pull out the "Document 1" and "Document 2" outside the window in flyout window,
3) UnPin the AutoHide button of the right side anchorable panel, with "Tool Window1" and "Tool Window 2", to make it closed on the right side,
4) put back "Document 1" inside the center document area of the main window
5) Mouse over on right side tab "Tool Window 1" to open the AutoHide window
6) Pin to disable the AutoHide of the "Tool WIndow 1",
7) The Anchorable pane with "Tool Window 1" and "Tool Window 2" is disappeared
I have tested it both with the default theme and the vs2010 Theme
1) run the sample TestApp,
2) pull out the "Document 1" and "Document 2" outside the window in flyout window,
3) UnPin the AutoHide button of the right side anchorable panel, with "Tool Window1" and "Tool Window 2", to make it closed on the right side,
4) put back "Document 1" inside the center document area of the main window
5) Mouse over on right side tab "Tool Window 1" to open the AutoHide window
6) Pin to disable the AutoHide of the "Tool WIndow 1",
7) The Anchorable pane with "Tool Window 1" and "Tool Window 2" is disappeared
I have tested it both with the default theme and the vs2010 Theme