I have the same problem cannot re-dock the "Snap Controls Bar" on "Inkscape 0.48.0 r9654" on Ubuntu 10.10.
In fact the toolbar was showing up as a separate window in my window list (i.e. the list of open windows in Ubuntu's panel).
The panel redocked when I right-clicked on the window list entry and selected close.
I have the same problem cannot re-dock the "Snap Controls Bar" on "Inkscape 0.48.0 r9654" on Ubuntu 10.10.
In fact the toolbar was showing up as a separate window in my window list (i.e. the list of open windows in Ubuntu's panel).
The panel redocked when I right-clicked on the window list entry and selected close.