Comment 29 for bug 171579

Quick test with Inkscape 0.48+devel r10817 + version 4 of the patch:
System: OS X Lion 64bit, gtk2/x11 2.24.8, gtkmm 2.24.2, default (new) preferences.
Custom Gtk+ theme based on Ubuntu's 'Ambiance' with minimal scrollbars mimicking the scrollbar overlay (no steppers, no minimal or fixed length of the slider).

If I quit Inkscape with dialogs minimized in the dock, I get erratic behavior the next time I launch inkscape. Initially, the dock expands to more than half the window size, while displaying the icons at the far right edge (it doesn't seem to matter whether the minimized dialogs display the dialog title as well or only the icon). Later on, after e.g. de-minimizing and closing the dialogs, they no longer reopen (visibly) in the dock (not as dialog nor as icon), but - when quitting and relaunching Inkscape - suddenly (but not consistently) some dialogs reappear as minimized icons.
I also experienced random changes of docked/undocked states which seemed to change without actually having undocked any dialog.

I'll do more tests next week, and try to provide 'steps to reproduce' for dialogs refusing to re-appear.

For the attached screenshot, I had opened and minimized 'Fill&Stroke', 'Layers' and 'Align&Distribute', quit Inkscape and relaunched it (initial document window size is set by a custom default template to window-width="1000" and window-height="650").